You know, it could also just be as simple as them naming the Pokemon based on what they hear.
What people shouldn't get mixed up as we have said over and over and over and over again
THE ANIME =/= THE GAMES
despite there being some relevant similarities, when judging over several cases is pretty silly. In the games this makes sense because Pokemon don't repeat their names as a cry, in spite of what they do, do in the anime
Seeing as Mewtwo was created by Man, it is ever so likely to abide to the name it is always referred to, that being said, the Mewtwo in the anime were pretty silent.