Hello, that’s exactly what happens to me sometimes! But only sometimes - I wasn’t able to isolate the problem yet but I have some suspicion. What stretching algorithm have you set up for that track? Do you use any signature changes in this project?
Anyway, I suppose there is just one workaround in this terrible situation: downmix the warped track stepwise by small chunks spanning only several bars. Then crossfade the resulting chunks together again. Nothing else worked for me… 
Best regards
Miloslav