This is kind of a hard thing to explain, so I made a video to show. First I moved via the engrave mode the lines to be more-or-less where they should be according to their rhythmic position (I had made them longer as a workaround to this bug) and then assign them to the actual position where I wanted them to be at, and I show that the bug moves things around when I do just that. Later I realized that the bug only happens if I assigned the lines to the pick-up bar so I just didn’t and then moved them via engrave mode to made it look like they actually were.
I’m not sure if I’m doing something wrong or what. I also saw in the video that you can see how some lines aren’t exactly where their rhytmic position is attached to, but that’s just because I moved some of them in Engrave Mode to try to make it look how I wanted it to. Even if I didn’t touch anything on Engrave Mode and every line was at its default position according to its rhytmic position, the bug would happen anyway (if there was a line attached to a rhytmic position inside the pick-up bar).
This is using multiple flows on the same page (the video shows the music content of Flow #3), but I think it happened to me once too in the past when it was just one flow.
Video link: https://www.youtube.com/watch?v=c4mxaCZwBoM