While large language model (LLM)-based multi-agent systems show promise in simulating medical consultations, their evaluation is often confined to final-answer accuracy. This practice treats their internal collaborative processes as opaque "black boxes" and overlooks a critical question: is a diagnostic conclusion reached through a sound and verifiable reasoning pathway? The inscrutable nature of these systems poses a significant risk in high-stakes medical applications, potentially leading to flawed or untrustworthy conclusions. To address this, we conduct a large-scale empirical study of 3,600 cases from six medical datasets and six representative multi-agent frameworks. Through a rigorous, mixed-methods approach combining qualitative analysis with quantitative auditing, we develop a comprehensive taxonomy of collaborative failure modes. Our quantitative audit reveals four dominant failure patterns: flawed consensus driven by shared model deficiencies, suppression of correct minority opinions, ineffective discussion dynamics, and critical information loss during synthesis. This study demonstrates that high accuracy alone is an insufficient measure of clinical or public trust. It highlights the urgent need for transparent and auditable reasoning processes, a cornerstone for the responsible development and deployment of medical AI.
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