This study evaluates the efficacy of vision transformer models, specifically Swin transformers, in enhancing the diagnostic accuracy of ear diseases compared to traditional convolutional neural networks. With a reported 27% misdiagnosis rate among specialist otolaryngologists, improving diagnostic accuracy is crucial. The research utilised a real-world dataset from the Department of Otolaryngology at the Clinical Hospital of the Universidad de Chile, comprising otoscopic videos of ear examinations depicting various middle and external ear conditions. Frames were selected based on the Laplacian and Shannon entropy thresholds, with blank frames removed. Initially, Swin v1 and Swin v2 transformer models achieved accuracies of 100% and 99.1%, respectively, marginally outperforming the ResNet model (99.5%). These results surpassed metrics reported in related studies. However, the evaluation uncovered a critical data leakage issue in the preprocessing step, affecting both this study and related research using the same raw dataset. After mitigating the data leakage, model performance decreased significantly. Corrected accuracies were 83% for both Swin v1 and Swin v2, and 82% for the ResNet model. This finding highlights the importance of rigorous data handling in machine learning studies, especially in medical applications. The findings indicate that while vision transformers show promise, it is essential to find an optimal balance between the benefits of advanced model architectures and those derived from effective data preprocessing. This balance is key to developing a reliable machine learning model for diagnosing ear diseases.