So since anime doesnt dictate anything in the games, lets use the games themselves. Each game takes place at different times or different places in the Pokemon universe, and for the sake of the argument lets assume you catch each legendary offered in each game. So in Red and Blue you caught Articuno Zapdos Moltres and Mewtwo. Then in Gold and Silver you caught them again but 3 years later and as a different character. These arent the same Pokemon, but just different ones of the species. So the Articuno Zapdos and Moltres you catch in Sinnoh and Kalos arent the same ones that live in the Kanto region. Mewtwo in Kalos is also a different Mewtwo. 3 confirmed different Mewtwo have existed.
At least this is my take on it and to me makes the most sense. Multiple Mewtwo seems like a strech, but if Mew "gave birth" once, why could it not do it again?
