Large language models fine-tuned via a two-stage pipeline (domain adaptation followed by instruction alignment) can exhibit non-trivial interference after adapter merging, including the re-emergence of explicit reasoning traces under strict decoding. We study this phenomenon in medical LLM settings using lightweight, reproducible measurements of trace leakage and instruction-following behavior. Beyond marker-based proxies, we introduce a marker-forbidden, answer-only evaluation and define a correctness-based direction that does not rely on surface markers; a rank-1 logit-space intervention along this direction modulates decision distributions and improves multiple-choice accuracy beyond random-direction controls at sufficiently large intervention strength. We further provide layer-wise geometric evidence that domain and instruction adapters induce partially misaligned update directions, and present a proof-of-concept geometry-aware merge that can reduce leakage and/or improve accuracy in a toy setting. Our results characterize boundary conditions of trace leakage and provide practical diagnostics and interventions for safer adapter merging.