This is bound to happen at least to some extent in most, if not all, curricula. From musculoskeletal last semester, I can recall one instance where our pathology prof went into so much detail on all the soft tissue tumors, etc., whereas they were barely touched in FA/Pathoma. I made sure to hit the high points in Pathoma hard, and then fit in what I could from class material for the most part. Despite lecturing on putative "minutia", I found that they still emphasize the same high points on the exams (i.e. the points FA/Pathoma emphasize). You just need to fine tune your studying in accordance with your professors, as it will be slightly different at every school. Just make sure you understand what's in Pathoma at the bare minimum, then go from there.