Studies that examine medical dispute cases (MDC) due to clinical reasoning (CR) are scarce in Taiwan. A retrospective analysis was undertaken to review MDC filed at four hospitals in Taiwan between 2011 and 2015. Cases were examined for the healthcare professionals involved, their relevance to CR errors, clinical specialties, and seniority. Seventy-eight MDC were identified and 57.7% of which were determined to be related to CR errors (n = 45). Among the 45 cases associated with CR errors, 82.2% (37) and 22.2% (10) were knowledge- and skill-related errors, respectively. The healthcare professionals with the most MDC were obstetrician-gynecologists (10/90, 11.1%), surgeons (8/90, 8.9%), and emergency physicians (7/90, 7.8%). The seniority of less than 5 years or lower had the highest number of attending physicians to be associated with MDC. In contrast, the highest seniority (>25 years) in the physician group and year 6 in the resident group are both shown with zero MDC. In our study, the larger hospitals had a significantly higher incidence of MDC compared to the smaller hospitals (Pearson Correlation Coefficient = 0.984, p = 0.016). An examination of MDC reveals the frequency and nature of medical errors in Taiwanese hospitals. Having identified that CR errors contributed a substantial fraction to the overall MDC, strategies to promote reasoning skills and hence reduce medico-legal issues help safeguard both patients and healthcare professionals.