Aside from Ultra Beasts, which look extremely bizarre on purpose, I can think of:
Dhelmise: a heavy anchor, obviously made of steel, which lives underwater but because of the seaweed on its body it's a Grass and Ghost type... wat?
Stunfisk and Falinks are really weird too. It's basically impossible to guess their actual types correctly the first time you see them.
I agree with Stunfisk and Falinks but Dhelmise has a point: you see, Dhelmise
isn't the anchor, it's the green seaweed that's more or less "possessing" the anchor. It's explained in the Pokedex entries. That's why it's Grass / Ghost and has Steelworker.
Mawile has never struck me as a Steel- or even Fairy-type. Maybe that's part of the deception? Apparently its fake mouth are overgrown steel horns, but what of the rest of Mawile's body? I've always found single-stage Pokémon like Mawile really weird because...why are they there? To make the dex more well-rounded type-wise? To give players more "good early-game, bad late-game" Pokémon?
I guess it's in part a logistics issue because drawing a lot of evolutions is complicated, and in part just for flavor I guess. Not everybody has to evolve. Snorlax is a good example of a single-stage Pokémon that's just good all the time.
I guess I never thought too much of Mawile, but if I had to guess the deception is probably the reason for fairy typing yeah.