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Koraidon and Miraidon were caught with modern day poke balls, that's how the time machine (allegedly) works, by sending a poke ball through time and recalling it. Even if that wasn't how they were caught, Koraidon (allegedly) pre-dates poke balls, probably by millennia, and Miraidon has no reason to be in a couple hundred years old poke ball. The ruins were also sealed before poke balls were invented.