Yeah, because they're rom hacks, for example:
Pokémon Prism remplaces Metapod with Shinx. So, if you transfer it using PkHex to Pokémon Sun... Surprise! It's a metapod! just with illegal attacks! like Spark, Charge, Bite, Roar, etc.
To prevent got banning from SuMo, just modify it like if it was like "legal" Pokémon.