I agree with you in theory, sure. But this isn't someone, say, posting a Doctor Who fic in the Final Fantasy section. That would be obviously wrong.
This isn't obviously wrong. Pokémon is primarily a videogame series. It makes sense that Pokémon fic ought to be posted in the Games section. Going to Anime to post videogame fic is incredibly counterintuitive.
Sure, you can blame people for posting a fic in a section that's obviously wrong. But just deleting a fic without a word of warning because it's posted in what seems to be the obviously correct place for it is just... that's just not right. Because, in this case, it's not the writer that's at fault, it's the site's obscure design (because, really, if you write a videogame fic, why would you go to Anime to check if it should be posted there instead of where all the videogame fic goes?).