Bukkit

What is the problem?
If you rebuild what somebody has done, it applies everything they have ever done, again, ignoring anything that happened after that. Example: person 1 destroys a tree. Person 2 places blocks where that tree was. I rollback person 1. I then rebuild person 1 and the blocks that person 2 placed are destroyed because person 1 at one point has destroyed the blocks located there.
What steps will reproduce the problem?

1. Rebuilding a person

What version of HawkEye are you using (shown in console during start-up)?
HawkEye v1.0.5b

Have you checked the FAQ page?
Yep

Ok so I understand your problem, but I am unsure as to how you think it should work - technically it is doing exactly what it is supposed to do - it is reapplying what the person did. If you want to make sure it does everything then you should restrict the rebuild by radius rather than player