Where Instruction Hierarchy Breaks: Diagnosing and Repairing Failures in Reasoning Language Models

As large language model (LLM) based systems take on high-stakes roles in real-world decision-making, they must reconcile competing instructions from multiple sources within a single prompt context. Enforcing an instruction hierarchy, where higher-level directives override lower-priority requests, is critical to the reliability and control of LLMs. In this work, we reframe instruction hierarchy resolution as a reasoning task. The model must first "think" about the relationship between a given user prompt and higher-priority instructions before generating a response. To enable this capability, we construct VerIH, a training dataset of constraint-following tasks with verifiable answers, comprising aligned and conflicting system-user instructions. We show that lightweight reinforcement learning with VerIH effectively transfers general reasoning capabilities of models to instruction prioritization. Our method leads to consistent improvements across multiple model families on both instruction following and instruction hierarchy benchmarks, achieving ~20% absolute improvement in conflict setups. Our method also leads to improved alignment to safety-critical scenarios beyond the training distribution, exhibiting increased robustness against jailbreak and prompt injection, reducing absolute attack success rates by up to 20%. Our results establish reasoning over instruction hierarchies as a practical mechanism for improving AI reliability, where targeted updates to system prompts produce predictable, controllable, and robust changes in model behavior.

Failures in language model reasoning emerge through distinct processes that leave identifiable signatures in the reasoning trace. We characterize these failures using token-level uncertainty signals, finding they arise through two empirically distinguishable processes. The first is committed failure, in which a model locks onto an incorrect reasoning path early in its trace. A central diagnostic signature is the commitment point, beyond which considering additional tokens hurt rather than help failure detection. In the second, persistent uncertainty, uncertainty instead accumulates throughout, and the full trace is needed to best distinguish failing from successful completions. These signatures reproduce across 23 model-dataset configurations, with the framework's falsifiable predictions holding in 20 of 23 cases, well above chance across both failure modes. Finally, we demonstrate our failure mode framework has direct implications for self-consistency, identifying when uncertainty signals complement it and when it can be selectively skipped. These results offer a foundation for understanding when LLM reasoning failures become detectable and for adapting detection strategies accordingly.

Language models are trained to follow instructions, but they are also powerful pattern completers. What happens when these two objectives conflict? We construct conversations in which a user instruction to behave in a target way T (e.g., always output a specific token, answer in a particular language, or adopt a persona) is opposed by N hardcoded assistant turns demonstrating a competing pattern P. We then measure instruction-following (IF) rates in this setting, across 13 models and 16 different instructions, for up to 50 turns. Average instruction-following rates range from 1% to 99% across models, largely uncorrelated with standard capability benchmarks. The transition from instruction-following to pattern-following is universal but highly model-dependent. Robustness is modulated both by instruction content, with models resisting induction longer when instructions align with their trained value priors, and by output format, with diverse multi-token responses proving substantially more resistant than single-token outputs. Chain-of-thought reasoning improves robustness but does not eliminate susceptibility, and can produce dissociation between correct deliberation and incorrect output. When asked to predict their behavior in this setting, models achieve 83.5% accuracy on average but systematically underestimate their own resistance to induction pressure. These results suggest that instruction-following remains brittle under induction pressure even for otherwise capable models, and that output diversity, rather than semantic engagement with the input, is the primary factor predicting robustness.