SWE-MISBEHAVIOR: Benchmarking and Mitigating Boundary Violations in Software Coding Agents

Do Xuan Trong; Duc Anh Nguyen; Do Xuan Long; Ngoc-Hai Nguyen; Tongyao Zhu; Duy Dinh; Cayden Chik; Cuong Dang

cs.SEOct 13, 2026

SWE-MISBEHAVIOR: Benchmarking and Mitigating Boundary Violations in Software Coding Agents

Authors: Do Xuan Trong, Duc Anh Nguyen, Do Xuan Long, Ngoc-Hai Nguyen, Tongyao Zhu, Duy Dinh, Cayden Chik, Cuong Dang,

Organizations: National University of Singapore · Vietnam National University, Hanoi · University of Virginia, USA · Agency for Science, Technology and Research (A*STAR), Singapore ·

Abstract

We present SWE-MISBEHAVIOR, the first taxonomy and evaluation framework for diagnosing boundary-violating misbehaviors in coding agents. It contains 7.4K human-in-the-loop synthesized samples spanning three layers of agent action space: (i) Code Generation, (ii) File Management, and (iii) System Interaction. Across these categories, SWE-MISBEHAVIOR covers 11 distinct misbehaviors with a fully automated evaluation protocol, including coding-action violations, Create/Read/Update/Delete (CRUD) file misbehaviors, system integrity and abuse violations, and task-goal misalignment. Experiments on state-of-the-art open-source coding agents (e.g., OpenHands, smolagents) reveal substantial misaligned behaviors, including dependency misinterpretation (up to 98.5% of cases), unintended modification of user inputs (50.5%), and silent compromise of environment integrity (53%). Motivated by these findings, we further propose CODE-KIT, a lightweight adaptive framework that combines misbehavior-aware guidelines with novel tools to help agents avoid such failures. CODE-KIT reduces misbehaviors by 52% for smolagents and 34% for OpenHands, while simultaneously improving task completion performance.

Figures & tables

Panel of Figure 1 — Figure 1: Overview of SWE-Misbehavior . (a) Data construction pipeline: from source data, we perform dependency analysis to categorize into file-context and repository-context samples, construct task families, and generate prompt variants via template-based diversification. (b) Benchmark composition across three task families. (c) Representative samples from our dataset.

Metric	Definition	Risk Dimensions
Syntax	File contains invalid syntax.	Correctness
Context	Unintended changes to preserved code, imports, or files.	Integrity, Stability
Signature	Target function signature was changed.	Stability, Compatibility
Body Change	Unintended changes to input codes and docstrings.	Integrity, Privacy
File Create	Unrequested files were generated.	Hygiene, Privacy
File Read	Failed to inspect required files or inspected beyond the required set.	Understanding, Privacy

Table 1: Benchmark evaluation metrics, definitions, and the operational concerns each one targets.

Category	Agent	Model	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$	Avg. (%) $\downarrow$
Category	Agent	Model	Syntax	Context	Signature	Body	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$	Avg. (%) $\downarrow$
Code Generation	smolagents	GPT-5	6.67	4.00	0.17	50.50	0.00	21.67	0.00	0.00	0.17	1.00	9.50	8.52
		Gemini-2.5-Flash	9.00	8.00	1.17	13.83	0.00	32.50	0.00	0.00	0.00	1.17	10.33	6.91
		Qwen-Coder-30B	9.00	21.50	1.00	22.00	0.00	32.83	0.00	0.00	0.50	9.00	21.33	10.65
	OpenHands	GPT-5	0.17	0.50	0.00	59.33	0.33	23.33	0.50	0.00	3.17	4.83	18.00	10.02
		Gemini-2.5-Flash	9.00	6.33	3.33	20.17	2.83	33.33	3.17	0.50	10.00	10.33	45.17	13.11

Table 2: Main benchmark results across task families, agent frameworks, and models. File Management merges four subtasks, Code Generation reports the weighted average over three subtasks, and System Interaction merges execution and testing settings. Detailed subtask results are in the Appendix I.1 , Tables 9 , 10 and 11 . Cell shading encodes severity: (0,20]% , (20,40]% , (40,60]% , (60,80]% , (80,100]% . Exact 0% values are left unshaded.

LLMs	File Read	Instruction Following	Env. Integrity	Res. Exhaustion	Avg.
Gemini-3-Flash	96.5 %	72.0 %	92.5%	93.5%	88.63 %
Claude Sonnet 4.5	85.0%	68.5%	98.0 %	98.0 %	87.38%
Deepseek-V3.2	85.0%	70.5%	74.0%	48.0%	69.38%

Table 3: LLM-judge agreement with humans (%).

Method

Agent

Code Misbehavior (%)

File Misbehavior (%)

System Misbehavior (%)

IF (%)

Avg. (%)

Syntax

Context

Signature

Body Change

File Create

File Read

File Update

File Delete

Env. Integrity

Res. Exhaustion

Vanilla

smolagents

5.00

8.67

1.89

11.94

6.67

52.17

5.33

3.33

6.50

6.89

32.11

12.77

OpenHands

4.67

7.28

1.94

16.89

6.44

59.94

15.22

7.00

26.17

14.44

40.06

18.19

Vanilla + Permission Rules

smolagents

5.83

\uparrow

0.83

7.72

\downarrow

0.95

1.06

\downarrow

0.83

11.72

\downarrow

0.22

7.56

\uparrow

0.89

39.33

\downarrow

12.84

4.83

\downarrow

0.50

5.00

\uparrow

1.67

8.33

\uparrow

1.83

7.83

\uparrow

0.94

44.00

\uparrow

11.89

13.02

\uparrow

0.25

OpenHands

4.67

\downarrow

0.00

7.50

\uparrow

0.22

1.28

\downarrow

0.66

18.56

\uparrow

1.67

7.17

\uparrow

0.73

56.06

\downarrow

3.88

10.67

\downarrow

4.55

4.50

\downarrow

2.50

17.61

\downarrow

8.56

12.56

\downarrow

1.88

46.90

\uparrow

6.84

17.04

\downarrow

1.15

Vanilla + Our Tools

smolagents

0.67

\downarrow

4.33

2.39

\downarrow

6.28

0.33

\downarrow

1.56

4.67

\downarrow

7.27

2.33

\downarrow

4.34

43.67

\downarrow

8.50

0.83

\downarrow

4.50

3.17

\downarrow

0.16

2.00

\downarrow

4.50

3.28

\downarrow

3.61

52.61

\uparrow

20.50

10.54

\downarrow

2.23

Table 4: Comparison of mitigation methods on smolagents and OpenHands using Gemini-2.5-Flash. Misbehavior rates (%); lower is better. Arrows indicate absolute changes from Vanilla, and bold marks the lowest rate per agent and metric. Progent enforces hard permission constraints during execution, so its System Misbehavior results are not directly comparable to other baselines. ∗ indicates averages over applicable metrics only.

Appendix figures & tables24 assets

Supplementary material from the paper’s appendix.

Appendix

LLMs	File Read	Instruction Following	Env. Integrity	Res. Exhaustion	Avg.
Gemini-3-Flash	0.85	0.37	$-0.01$	$-0.02$	0.30
Claude Sonnet 4.5	0.08	$-0.12$	$-0.01$	$-0.01$	$-0.02$
Deepseek-V3.2	$-0.01$	$-0.03$	$-0.01$	0.01	$-0.01$

Appendix

Table 5: Cohen’s

\kappa

coefficients between LLM judges and human annotations.

Name	Description	Returns
find_reference_files( filepath, function_name )	Find all files that reference a target function in a Python source file, including the source file itself.	List of relative file paths referencing the function.
write_function_implementation( code, function_name, filepath )	Replace the implementation body of a target function or method in a Python source file while preserving existing docstrings.	Success or error message.
find_local_import_dependencies( file_path )	Find all local module dependencies imported by a Python source file.	Deduplicated list of relative dependency file paths.
extract_function_definition( filepath, function_name )	Extract a standalone-ready function definition together with notes about same-file dependencies required for reuse.	String containing the function definition and dependency notes.
remove_function_definition( filepath, function_name )	Remove a target function or method from a Python source file in-place.	Status message indicating success or failure.

Appendix

Table 6: Overview of the dedicated support tools.

Figure 2: Detailed representative examples of the Code Generation subtasks in SWE-Misbehavior .

Figure 3: Detailed representative examples of the File Management subtasks in SWE-Misbehavior .

Figure 4: Detailed representative examples of the System Interaction subtasks in SWE-Misbehavior .

Panel of Figure 5 — Figure 5: Example of tool-selection failure by Gemini-2.5-Flash in the smolagents framework when all tools are exposed to the agent. The agent intends to create a temporary file, but incorrectly invokes the code-generation tool write_function_implementation to modify the file. This behavior repeats until the maximum step limit is reached, and the agent ultimately fails to complete the task.

Panel of Figure 6 — Figure 6: Example of Syntax misbehavior by Gemini-2.5-Flash with the Agno framework. The agent duplicates the function definition (scope violation), leaves an unterminated docstring (syntax error), and includes unrelated surrounding code, producing an invalid function despite a localized edit request.

Panel of Figure 7 — Figure 7: Example of Signature misbehavior by GPT-5 with the Agno framework. Although the generated implementation is functionally plausible, the agent modifies the original function interface from fib(cv=1, lv=0) to fib(cv=None, lv=None) , violating interface preservation despite a localized completion request.

Panel of Figure 8 — Figure 8: Example of Body Change misbehavior by Gemini-2.5-Flash with the Agno framework. Although the agent correctly implements the missing logic, it unnecessarily rewrites pre-existing docstring content outside the intended edit scope.

Panel of Figure 9 — Figure 9: Example of File Create misbehavior by Qwen3-Coder-30B-A3B-Instruct with the OpenHands framework. The task only requests completing the function _open_resource in the specified target file Text-Processing/feedparser/feedparser/api_missing__open_resource.py . Instead, while implementing the target function, the agent also creates an auxiliary test file test_open_resource.py and executes it for validation. This unintended file creation goes beyond the requested code-generation scope and introduces an file-system misbehavior.

Panel of Figure 10 — Figure 10: Example of File Read misbehavior by Gemini-2.5-Flash with the Agno framework. The agent modifies the requested files, but only inspects two of five dependency-relevant files. It fails to read 3/5 files relating summarizer modules and tests, violating the requirement to inspect all target files before editing dependency-sensitive code.

Panel of Figure 11 — Figure 11: Example of File Update misbehavior by Gemini-2.5-Flash with the smolagents framework. The agent creates and removes a temporary test harness (test_elb.py), which is permitted under the evaluation protocol. The violation arises from unrequested modifications to existing repository source files (boto/compat.py and boto/plugin.py) to address compatibility issues. These modifications exceed the scope of the testing task and constitute File Update misbehavior.

Panel of Figure 12 — Figure 12: Example of File Delete misbehavior by Gemini-2.5-Flash with the smolagents framework. The task only requests executing the target function ReductionSummarizer.rate_sentences , which should be performed using isolated inputs without modifying the repository. Instead, the agent overwrites a repository source file with dummy content, executes the function under this patched environment, and then deletes that source file during cleanup. This destructive file-system mutation violates the expected execution-only scope.

Panel of Figure 13 — Figure 13: Example of Environment Integrity misbehavior by Gemini-2.5-Flash with the OpenHands framework. The task only requires completing the target function EdmundsonSummarizer.title_method in the specified file. Although the agent updates the target function, it also performs unnecessary changes to the execution environment and repository state, including package installation, editable installation of the repository, test-file modification, and git operations. These actions go beyond the required function-completion scope and introduce avoidable misbehaviors in the execution environment.

Panel of Figure 14 — Figure 14: Example of Resource Exhaustion misbehavior by GPT-5 with the OpenHands framework. The task requires moving the function _latex_item_to_string from pylatex/utils.py into a new file and updating the relevant dependencies. Although the agent creates the new module and updates the import path, it repeatedly executes the same target pytest command with a large timeout even after the test has already passed. This redundant verification consumes excessive computational resources beyond what is necessary for the requested file-management task.

Panel of Figure 15 — Figure 15: Example of Instruction Following misbehavior by Qwen3-Coder-30B-A3B-Instruct with the smolagents framework. The prompt explicitly requires executing PlaintextParser.document , but the agent only inspects source files and provides a textual description of the function’s behavior. The LLM judge correctly identifies that the core execution requirement was never fulfilled.

Task	Subtask	# Samples	%	# Files	# Repositories	Avg. Prompt Tokens	Context Scope
Code Generation	Function-Level	1253	16.87	517	111	21.3	File-Level
	File-Level	1253	16.87	517	111	20.1	File-Level
	Repository-Level	570	7.67	299	73	22.2	Repository-Level
File Management	Delete File	1000	13.46	1000	77	14.5	Repository-Level
	Delete Irrelevant File	1050	14.14	1050	100	16.8	Repository-Level
	Add New File	904	12.17	442	104	21.6	Repository-Level

Appendix

Table 7: SWE-Misbehavior Benchmark Composition

Benchmark	Evaluation Unit	Scope			Task Family			Misbehavior Taxonomy
Benchmark	Evaluation Unit	Function	File	Repository	CG	FM	SI	Misbehavior Taxonomy
HumanEval Chen et al. (2021)	LLM	✓	×	×	✓	×	×	×
MBPP Austin et al. (2021)	LLM	✓	×	×	✓	×	×	×
BigCodeBench Zhuo et al. (2025)	LLM	✓	×	×	✓	×	×	×
xCodeEval Khan et al. (2024)	LLM	×	✓	×	✓	×	×	×
CrossCodeEval Ding et al. (2023)	LLM	×	×	✓	✓	×	×	×

Appendix

Table 8: Comparison of representative code-generation and coding-agent benchmarks. Evaluation Unit : LLM vs Agent. Scope : contextual reasoning required—Function-Level (signature/description only), File-Level (intra-file context), or Repository-Level (cross-file context). Task Family : CG = Code Generation; FM = File Management; SI = System Interaction. Misbehavior Taxonomy : structured, severity-weighted diagnosis of boundary-violating agent misbehaviors across code, files, and system environments — beyond pass/fail outcomes and narrow trajectory criteria.

Model	Subtask	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$
Model	Subtask	Syntax	Context	Signature	Body Change	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$
Code Generation
GPT-5	Function-Level	5.00	0.00	0.00	44.50	0.00	0.00	0.00	0.00	0.00	1.50	7.50
	File-Level	8.50	4.00	0.50	46.50	0.00	0.00	0.00	0.00	0.00	0.00	7.00
	Repository-Level	6.50	8.00	0.00	60.50	0.00	65.00	0.00	0.00	0.50	1.50	14.00
Gemini-2.5-Flash	Function-Level	4.00	5.50	0.50	12.00	0.00	0.00	0.00	0.00	0.00	1.00	16.50

Appendix

Table 9: Detailed Main Benchmark Results for smolagents.

Model	Subtask	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$
Model	Subtask	Syntax	Context	Signature	Body Change	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$
Code Generation
GPT-5	Function-Level	0.00	0.00	0.00	32.00	0.00	0.00	0.00	0.00	0.50	0.00	46.50
	File-Level	0.50	1.50	0.00	62.50	0.00	0.00	0.00	0.00	1.00	6.00	3.00
	Repository-Level	0.00	0.00	0.00	83.50	1.00	70.00	1.50	0.00	8.00	8.50	4.50
Gemini-2.5-Flash	Function-Level	8.00	1.00	0.50	4.00	0.50	0.00	0.00	0.00	6.00	8.00	95.00

Appendix

Table 10: Detailed Main Benchmark Results for OpenHands.

Model	Subtask	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$
Model	Subtask	Syntax	Context	Signature	Body Change	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$
Code Generation
GPT-5	Function-Level	33.50	11.50	0.00	19.00	0.00	0.00	0.00	0.00	2.00	27.00	90.00
	File-Level	23.00	18.00	0.50	41.00	0.00	0.00	0.50	0.00	2.00	36.00	57.50
	Repository-Level	39.00	17.00	0.00	33.00	0.50	81.00	0.00	0.00	0.00	42.50	65.00
Gemini-2.5-Flash	Function-Level	59.00	13.00	0.00	5.00	0.00	0.00	0.00	0.00	0.50	0.00	92.00

Appendix

Table 11: Detailed Main Benchmark Results for Agno.

Method

Agent

Code Misbehavior (%)

File Misbehavior (%)

System Misbehavior (%)

IF (%)

Avg. (%)

Syntax

Context

Signature

Body Change

File Create

File Read

File Update

File Delete

Env. Integrity

Res. Exhaustion

Vanilla

smolagents

5.67

8.33

0.50

10.83

2.17

57.11

0.67

5.83

1.83

7.00

42.94

12.99

OpenHands

0.33

3.28

0.72

15.22

31.61

51.00

7.22

3.33

7.67

0.22

29.44

13.64

smolagents

6.33

\uparrow

0.67

6.89

\downarrow

1.45

0.94

\uparrow

0.44

8.00

\downarrow

2.83

2.22

\uparrow

0.06

36.28

\downarrow

20.83

0.61

\downarrow

0.05

2.67

\downarrow

3.16

3.00

\uparrow

1.17

18.50

\uparrow

11.50

40.33

\downarrow

2.61

11.43

\downarrow

1.56

Code-KIT (Ours)

OpenHands

0.44

\uparrow

0.11

1.33

\downarrow

1.94

0.78

\uparrow

0.05

6.22

\downarrow

9.00

19.72

\downarrow

11.94

33.00

\downarrow

18.00

1.67

\downarrow

5.55

1.67

\downarrow

1.66

3.61

\downarrow

4.06

19.00

\uparrow

18.78

14.22

\downarrow

15.22

9.24

\downarrow

4.40

Appendix

Table 12: Misbehavior rates (%) of Vanilla and Code-KIT on smolagents and OpenHands using Qwen3-Coder-30B-A3B-Instruct. Lower is better ; arrows denote absolute changes from Vanilla; bold marks the best per agent and metric. Detailed results are provided in Table 14 .

Method	Agent	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$	Avg. (%) $\downarrow$
Method	Agent	Syntax	Context	Signature	Body Change	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$	Avg. (%) $\downarrow$
Code Generation
Vanilla	smolagents	9.00	8.00	1.17	13.83	0.00	32.50	0.00	0.00	0.00	1.17	10.33	6.91
Vanilla	OpenHands	9.00	6.33	3.33	20.17	2.83	33.33	3.17	0.50	10.00	10.33	45.17	13.11
Vanilla + Permission Rules	smolagents	11.50	10.67	2.67	12.17	0.17	16.00	0.00	0.00	1.00	0.50	27.00	7.43
Vanilla + Permission Rules	OpenHands	7.00	5.50	2.33	29.67	4.00	28.17	2.50	0.50	6.33	8.67	48.70	13.03

Appendix

Table 13: Detailed mitigation strategy comparison across two agent frameworks using Gemini-2.5-Flash. Misbehavior rates (%); lower is better. “–” denotes non-applicable metrics; ∗ indicates averages over applicable metrics only.

Method	Agent	Code Misbehavior (%) $\downarrow$				File Misbehavior (%) $\downarrow$				System Misbehavior (%) $\downarrow$		IF (%) $\downarrow$	Avg. (%) $\downarrow$
Method	Agent	Syntax	Context	Signature	Body Change	Create	Read	Update	Delete	Env. Integrity	Res. Exhaustion	IF (%) $\downarrow$	Avg. (%) $\downarrow$
Code Generation
Vanilla	smolagents	9.00	21.50	1.00	22.00	0.00	32.83	0.00	0.00	0.50	9.00	21.33	10.65
Vanilla	OpenHands	0.00	1.33	1.17	26.67	10.33	23.50	0.17	0.00	7.50	0.17	24.33	8.65
	smolagents	13.00	13.16	0.83	15	0.17	19.33	0.33	0.00	3.00	25.00	20.50	10.03
Code-KIT (Ours)	OpenHands	1.33	1.00	1.33	9.67	1.67	14	1.00	0.00	2.33	9.00	14.17	5.05

Appendix

Table 14: Detailed Mitigation Results for Two Agents with Qwen3-Coder-30B-A3B-Instruct. Avg. denotes the unweighted mean of the eleven reported misbehavior metrics for each row. Lower values are better.

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