I started playing around with Pokémon Go and caught a couple of Pokémon. They're showing up in the Pokédex but not in my Pokémon. Did I delete them or something by accident and is there any way to get them back?
I had the same thing happen with Wigglytuff: I did not have the Pokemon, but it was in my Pokedex. When I got an actual Wigglytuff, I didn't receive 500 XP for the initial Pokedex find.
It is most likely you transferred the Pokemon because it was weak. If you did so, there is no way to get it back.
It's also possible that this is a bug. The bug happened for a few of my friends, but it has likely been fixed, so I believe it's more likely you simply transferred it.