I want to clone multiple Pokemon a once - is this possible? This is for X and Y
As far as I know cloning is done by trading a Pokemon and then doing some trickery to glitch the game and clone the Pokemon. Since you cant trade more than 1 Pokemon at once, you cant clone more than 1 Pokemon at once.
Unless you can trade more than two Pokémon at a time this is impossible, as one Pokémon disappears.
Source: Logic