I remember a vanilla bug which has the same symptoms but I'm wasn't able to find its ticker on mojang's issue tracker, so I can't verify if it's from before 1.8.9 or if 1.8.9 is affected by it as well.
Could you please upload the replay file somewhere and give exact instructions on how to reproduce this?
Hint: Placing markers on the timeline by pressing M will help with exact reproduction because one can click them to get to the exact time and place of where they've been placed.