Hmm...
Dunsparce. I kept thinking it's a Ground type. But no, it's Normal >.>
Bibarel. Yes, it may be some sort of beaver thing, but I never expected it to be part Water. Plenty of Normal types can learn moves like Surf anyways (like Linoone).
Azurill. You do not know how many times I've tried using Grass/Electric type moves just to realize hey, it's not a Water type.
Drapion. OK, really, it's Dark/Poison, and yet Aaron has it on his team. Sure, Skorupi is part Bug, but that makes you think Drapion is a Bug type too. It even LOOKS it, for heavens sake! Bug/Poison would probably be a better combo for it, if you ask me >.>
Pachirisu. Just because it had some blue I thought it'd be Ice and not Electric XD But I found out it was indeed Electric after watching the episode Dawn/Hikari gets one. This was pre-DS/Pearl for me, by the way.
Kingdra. I continued thinking it was just Water and in no way part Dragon XD But of course, that's different now~
Girafarig. When I tried using a Ghost move against it and it failed, I realized it was part Normal. I always thought it was purely Psychic.
Barboach, Whiscash, and Quagsire (and maybe Wooper). They don't really seem like Ground types too much, compared to Marshtomp/Swampert.
I'll probably think of more later :X