Moves that are learned only in the first generation games, that can be legally traded back and forth between Gen 1 and 2 on VC or otherwise are being flagged as illegal. Legendary PK1 files directly inserted into a Gen 2 game are also being flagged illegal. Nothing is edited on the Legendaries, these are captured and trained in-game. The Mew is an unedited copy of the GF Mew and was previously legal in the last version of PKHeX.