>>31582509No, but for a time, Rotom's alternate forms were counted as illegal pokemon. Not sure if they fixed that yet.
As for the others, if you transfer a pokemon from Gen 1 and evolve it into a cross-gen evo, like Porygon2, Scizor, Crobat, Electivire, etc, it is now an illegal pokemon. Because you can't obtain those pokemon in the Gen 1 VC
And if you bred an island scan species with its HA in Alola (like Contrary Serperior or Shadow Tag Gothitelle) it is an illegal pokemon, because island scan pokemon can't have HAs.