Mewtwo's 'Forme' (now confirmed as mega evolution). They would have been told about it by GameFreak. As I'm aware of things, GameFreak do not add things or do things because the anime did it first. gameFreak created Mega Mewtwo and the ones that created the last movie decided to feature Mewtwo and his transformation.
That being said, I never specified that the Anime canon has no connections to game canon at all. However, they are still both separate canons, and I'm sure we all agree here that game canon is the 'true canon.'