This happens with two-ply rolls. When the roll is started, i.e., the end is unstuck from the roll, one ply was unwound more and is now out of synch. The solution is to unwind the second ply so that its perforation matches the perforation of the other ply.

Obviously, in addition to being obsessive, I also spend too much time in the bathroom but, hey, it's an important part of life and I do enjoy a good dump.