Okay so I usually keep a couple of Shiny Manaphys /Regular Manaphys from Gen 4 in my PC, as well as a legit one that was redeemed by a trusted person. They had the legal check mark on the previous PKHeX version. The one I am displaying now is the legit one.
This is the original one, unedited. It shows this alert.
Then I changed the Ability to Hydration 2, it shows Hidden Ability mismatch
And when I set it to to Hydration (H), it shows the same thing as the first one.
Is there some sort of glitch with PKHeX or my Pokemon? There shouldn't be any problem with the Manaphy but as you can see, there is.
