What are the primary causes of conflict between PhD advisors and their students? 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.
The biggest causes of conflict, beyond personality-related issues, I believe stems from a point made in the linked article—lack of communication.

When advisors and advisees are not on the same wavelength, either because goals have not been clearly communicated, or because the frequency or quality of contact and correspondence between the two has broken down, conflicts can result. This is especially true when it comes time to graduate: the advisor may have specific expectations on what the student is required to provide; however, unless this is directly communicated to the student, there will potentially be a lot of conflict in getting to a point where both are satisfied with the final results.

Often, this can be solved by having a direct discussion about the unresolved issues. However, if there is a pathological problem—in other words, one that can't be resolved through communication between the student and advisor—it may become necessary to invoke the thesis committee, graduate officer, department chair, or other authority who can help to resolve the problem.