Yes, this happens with most VC Pokémon now. The only exceptions I've found being:
Kanto starters.
Kanto fossils.
Kanto legendaries.
Nidoran family, save for both Nidoran themselves.
Cross-generational evolutions (save for gen 2 introduced cross-gen. For example, a G1 VC Leafeon is flagged as legal, but an Espeon from the same origin isn't, though Kingdra seems to be okay).
Pikachu, Raichu, Vulpix, Ninetales, Hitmonlee, Hitmonchan.
What they have in common is that, breeding aside, most of them aren't normally obtainable in GS, so my guess is that PKHeX properly takes them as being from Kanto, but any other Mon is flagged as being from Johto (even if they have the RBY game ID in their data), and therefore, illegal.
They need at least one G7-introduced ribbon in order for the legality issue to be triggered, though. Which means, the Effort, Footprint and Best Friend ribbons will not trigger it, but the Alola Champion, Battle Royal, and both Battle Tree Ribbons, will do.
I noticed this quite a while ago, but didn't feel the need to say it since I expected it to be corrected in some update, but since someone else is adressing it now, I thought I might as well say what I had found out.