Don't you guys remember this is a new Mewtwo? It even had a special anime episode (which we will probably not be getting) which explains its origins. Don't know any specifics, I just know it's a second Mewtwo that was created for some reason.
And if the games can have multiple Mewtwo's why not the anime? We know that at least 3 Mewtwo exist: The one from Cerulean Cave (though the continuity of that one is up for questioning since it appears in HeartGold & SoulSilver), the one that was on the Sky Fortress in the Pokemon Ranger games, and one that is in the Pokemon Village in XY. Of course I suppose you can argue that after Gold/Kris/Soul disturbed it at Cerulean Cave it moved out of Cerulean Cave, got caught by the Societea caught Mewtwo and was just keeping it in suspended animation until they needed it, and after it was freed it fled to the Pokemon Village in Kalos.
Then we have to question the continuity of the Mystery Dungeon games which all have Mewtwo in it as well as the one that appears in Pokemon Conquest even though that game takes place before modern science.
Let's just assume that as long as you have some Mew DNA and a mad scientist, you can probably create a Mewtwo who will no doubt go berserk and escape. 