Connected clips going out of sync [BUG/ISSUE?]

I have noticed a couple of times now, a bug in Final Cut Pro which seems to shift my connected clips, both sound and video, out of sync. I usually notice it when I try to override to primary storyline, and the video moves to a weird place:

So this: ibb.co/9YjGt13

Becomes this: ibb.co/y5D4Z5j

Instead of this: ibb.co/hML5Wcr

Does that make sense? How I usually am able to fix this is by copying all of the project into a new project, and edit from there. But what happens then is that a lot of black 1-frame gaps are added (as seen here: ibb.co/QCd0smG ), between every clip, and the connected clips go out of sync (in this case 6 frames, corresponding to the six black frames).

I have experienced this on two seperate projects, across two different production houses, with different versions of FCPX. I have a suspicion that it has to do with mixed framerate (although I dont think there's any on this project) or maybe XML import, but I am not sure. Anyone have any exeperience with this?