Flagging my Milotic from Emerald (possible bug?)

[personguy]

Pkhex seems to be taking issue with my Milotic here, which I won contests with in Emerald then transferred through all the way up to BD. Not sure why it is flagging, it's actually completely legit! Pkhex seems to think there's a fateful encounter problem, or just an encounter mismatch?

350 - Milo - 621E6367DBE5.pb8

[Nuren]

Known issue that we call "evotree". Basically, PKHeX doesn't account for changes in evolution methods between games. This will be fixed eventually, just not soon.

You can read here if you want to know how big the problem is and what all has to be accounted for to fix it properly:
https://github.com/kwsch/PKHeX/pull/3359#issuecomment-1003808371