I rendered a video using Optical Flow (it includes lots of Time Remapping). Basic cuts look as if there was a short glitch-like transition between them.
Frame of first shot [1
Did you apply the Optical Flow to a nested sequence that contains a transition? This looks to me like Optical Flow trying to invent new frames to fill in the slow motion and getting confused by the fact that a transition is blending two different videos. You should apply your time remaps to the base clips and then do transitions on top of the already adjusted clips.