PokéBase - Pokémon Q&A
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For example, you have just received the National Pokedex in Platinum, and you go to the Battle Factory. You battle a Zangoose. Will it get added to the Pokedex?

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No they do not get added.

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This is one of the most annoying parts of the games. Why can't they get added, it doesn't make sense!
I agree if they did my pokedex woud get alot bigger and I do not think it is fair that the bosses get to use ubers and the challenger can't