Seems like the save glitched out. Maybe try using the reader to completely delete your save. I’ve had similar stuff happen to my Crystal save before (mons appeared in my PC, and the corruption spread, overwriting other PC slots), and even wiping the save in-game carried the glitchiness over to a new save.
Tho, if wiping the save using the reader didn’t fix it, then it’s possibly a cart issue.
[to elaborate, I originally gave up a PC box to corruption, and it stayed for a while. Like I was able to play normally after forsaking that one box. But eventually I noticed some mons going missing, as tho the corruption spread]