Idk if yours ended doing that through casual cheating or something completely different... sounds like through cheating tbh. :p
... if you don't get rid of that Bad EGG right away, then store it in either BOX3 or BOX6 *Only* with no pokemon in them either. Especially useful if you end up with multiple Bad EGGs at once.
If I were you, put those mon in sinnoh box instead. Delete All previous cheats you used (if you have any remaining)