Here's a very interesting analysis from a professor's point of view on the primary causes of conflict between PhD advisors and their students:
In my experience, incompatible personalities account for a large fraction of the conflicts that I have run across over my 13 years since college. Basically, the student has the wrong advisor. No one is at fault – it's like a marriage that doesn't work out.
I would like to get some more perspectives on this question though, as graduate students may perceive this question differently.
I've observed three main failure modes:
- Different research interests. Even if nominally in the same subfield, it's difficult to work on a years-long project if both advisor and advisee are not really engaged. Both will try to subtly pull the project in a more interesting direction, and it's easy for both to have a different understanding of what the goal is.
- Different working styles. If the professor expects 9-5 hours and the student likes to work in the middle of the night, there may be conflict. Or, the professor may be interested in rigorous theory while the student takes an "if it works, it works" attitude. The latter can be a good opportunity for learning, but it can also just lead to conflict.
- Poor behavior. Laziness and abusiveness are difficult to negotiate. Note, this goes in both directions - plenty of examples of diligent students with lazy professors.
I agree with @aeismail that basically all of these can be resolved by better communication (and exacerbated by poor communication). It's sort of counter-cultural to do performance reviews and written-down goals, but it's not a bad idea, at least occasionally.
Edit: just realized this was 6 years old. But, the question was recently modified, so I'll leave my answer.