It happens to almost everyone at some point.

It happened to me on my general surgery rotation. I showed up on time, worked hard, helped the team whenever I could, volunteered for whatever I could get my hands on, got along with everyone, and was never told there were any issues. A few months later I get a copy of my eval and I was given the lowest possible grade above failing. I was graded by the chief resident, whom I spent only 2 weeks with and had absolutely no problems with (I thought she was cool with me). She put a few criticisms in the written comments, but absolutely nothing that indicated I was a student that deserved to barely pass, and the ratings on the individual sections (like knowledge, professionalism.. etc) were average or above average in general, so giving me an overall barely pass made no fucking sense.

Mind you, I knew I wasn't interested in gen surg at this point so it shouldn't really bother me, but I was furious because I knew that I absolutely did not deserve this. I have never complained about anything during med school, but this pissed me off enough to schedule a meeting with the chair of surgery at the school. He basically told me that some residents can be assholes, and that as long as this was an outlier, nothing from the eval would be on the Dean's Letter and it would just affect my overall surgery grade a bit (because it was 8 weeks and there were 2 other evals). Once I knew that this wouldn't somehow fuck me up for residency, I was OK with it (nothing else I could do anyways), and I just moved on. Sure enough, when I got me Dean's Letter copy, nothing about that eval was there.

Moral of the story, just let it slide, and if you feel that it could really affect you negatively, meet with the head of the department and let them hear your concerns.