I solved this by clicking "Video" then "Match Source" while exporting. It had 29.97 FPS set there on the problematic exports. EDIT: Although in the timeline this still occurs. If I notice it on the proxy version and untick proxy, it's not on the original. I have some sort of seeking problem for some reason. I'm not seeing the overlapping image anymore between clips on the exported video so it's sort of solved.
