One issue I've seen a few times is that some commit in the middle of a topic branch is the problem, but if you didn't rebase it then that commit itself would look fine on top of the topic branch's parent. However, after merging it's now also on top of other commits, and the interaction with those was the problem. That makes it very hard to find such a problem. Rebasing the history of the topic branch before merging will make finding it much easier.