If you just let the track play to the end without touching anything, it will play without errors. I'm not sure if this is always the case, but it has been for me this far. As soon as you change the view during the replay, you can't go back to the original recorded track view, and the track gets messed up.
Because of that I always save additional backup track which stays untouched when the other one gets messed up.
I don't know why this issue has remained for so long without being fixed. This is where Eagle Dynamics can probably learn something from 1C Game
Studios and their IL2 series. Their replay tracks work perfectly. Maybe methods they use can not be applied in DCS without changing lot of things.
Also, it would be nice to have the IL2's "Track view" which, after changing the view during track playback, brings you back to the original recorded gameplay view and original head movements.