Hello! I noticed that with the latest PKHeX version (20250223) a lot of Pokémon in my Pokémon X save file are shown with the red triangle, but they actually legal (normally caught in-game).
This does not happen with PKHeX ≤ 20241111
(Here a Karrablast for example)
Ok, I see that the problem is related to the new "PP verifier"
As changelog said, every Pokémon that has not been healed since capture is flagged as illegal.
I tried catching a few mons to verify and yes, every Pokémon that used a move during the fight is marked. However, in-game the PP count is always shown "full".
Picking the Pokémon from the Box and then depositing it restore the PP count and PKHeX flagged the mon as legal.