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Already caught mewtwo?

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on Pokemon x and y when I go to mewtwo cave I drain his health really low and when I got to use my ultra ball it tells me it has "it seems to be caught" what do I do

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That is a message you get sometimes when a Pokemon breaks out of the Pokeball, just keep throwing the Pokeballs and it will stay in eventually.

EDIT: If you meant "It appeared to be caught." then this is the reason. Otherwise I wouldn't really know what, maybe the message got replaced.

Source: Experience

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ok thanks ill try that