Justin-
There are a few things potentially causing this.
1) Since you say the proxy media is not displaying this, then I would guess that long GOP format clips (h.264) can behave this way when optical flow retiming is applied on the proxy media (Pro Res 422 1/4 res scaled to full frame- a non long group of pictures codec) and then you switch to the original media, the the interpolation markers that optical flow retiming is looking for aren’t in exactly the same places….
and
2) iPhone frame rate is variable. BOOM.