Maybe those were illegal but because the legality check wasn't detecting them as so, you didn't notice it. When the legality check was updated, it detected those illegal things that it did not detect before.
Hello, first post here to talk a little bit about myself. I am 15 and I'm gonna be 16 in 19 days! I beaten 3 Pokémon games: FireRed, Emerald and Black. I am Argentinian and I'm gonna be glad to help in everything I can!