If you’ve used the segment tool to cut/paste segments, it can result in segmentation of the bounce tracks. This is a point on my todo list that I intend to improve in the future. Hidden bounce tracks really shouldn’t be chopped up like the regular audio tracks.
You can verify this problem by right-clicking the wide “Bounce” button in the master track group in the track inspector rack, and deselect “Hide track lane”. To clean up the bounce track, deselect the bounce mode on the master track, and then redo the bounce.