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I always assumed they were turned into light. I figured real life solutions can be disregarded since it is a fantasy world where our logic is very flawed. The Pokemon can be turned into light energy when caught, they were turned into light energy. The Pokemon can escape and make the ball unusable by shattering one of the mirrors while bouncing around frantically. I admit it was not my idea, but it's the one that makes the most sense considering canon Pokeballs have that inside.
