What did I do wrong with audio snap

[KSband]

I wanted to line up my bass notes with the drum track so I changed both tracks to audio transients and stretched or shrunk the bass notes to line up. It all sounds good except.... not every time but once in a while the bass will go out of sync in the same spot. When I pause and go back to try and find the exact place it sounds fine again. It's very weird and I've done this editing a lot of times with no problems. Maybe I did something wrong this time?