Evaluation of medical artificial intelligence agents remains predominantly answer-centric, assessing only the correctness of final outputs while overlooking the quality of intermediate reasoning. In clinical settings, however, a correct answer reached through fabricated evidence or incoherent logic is as dangerous as an incorrect one. We propose MedTraj, a framework that treats reasoning trajectories as critical objects for construction, evaluation, and optimization. The pipeline generates structured multi-step clinical reasoning chains from medical diagnosis sources. Each trajectory is then parsed into clinical observations, evidence, numbered reasoning steps, and a final conclusion, and scored across five quality dimensions: coherence, evidence support, hallucination, completeness, and traceability. Controlled error injection introduces targeted faults into otherwise correct trajectories to establish causal links between specific reasoning failures and measurable quality degradation. Building on this, step-level filtering based on marginal contribution identifies which individual reasoning steps drive or undermine trajectory quality. Finally, quality-weighted context learning feeds trajectory evaluations back into the model at inference time, allowing it to learn from both strong and weak reasoning demonstrations. Experiments across CareQA, PubMedQA, and CECMed demonstrate that trajectory context consistently improves reasoning coherence, with gains of +0.029 to +0.041 over a zero-shot baseline. On the CECMed severity assessment task, quality-weighted context nearly doubles the correctness over the zero-shot baseline while cutting the hallucination ratio by 87%. Marginal-contribution analysis further shows that a small minority (15.3%) of reasoning steps carry most of the quality signal, and that extending chains beyond four steps yields diminishing returns.

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