Ghost/Missing notes in PDF Import?

So I was transferring all my scores from FLAT to Musescore because the account I use for Flat will be shutting down soon and I didn't want to lose all my work. but when I opened up the score in Musescore, there are entire sections missing for each instrument, some rests are colored grey, and there are even rests where there shouldn't be! It's a 3/4 time signature, but there's plenty of instances of a 4th "ghost rest" popping up in the middle of measures and I can't figure out how to delete them. Anybody have an idea??