Quite a few on my mind:
Porygon family: Steel - at least GameFreak have retyped the Magnemite evolutionary family, but why not these three?
Beedrill: Poison/Flying - It is poisonous, but why can't this bee escape from Ground-type moves?
Gyarados: Water/Dragon - It certainly looks like a dragon, but it's unusual having the added 'Flying' type.
Vibrava & Flygon: Bug/Ground - They look like dragonflies, so that means they should be bug-type.
Darmanitan: Fire/Fighting - It has huge fists, so it could've forged new ground as the first non-starter Fire/Fighting Pokemon.
Shellos & Gastrodon: Water/Poison - Sea Slugs look poisonous, and due to the fact that they learn poison-types moves makes me wonder.
Golett & Golurk: Ghost/Steel - It's armor is made of metal, so why doesn't it get STAB on Heavy Slam?
Not to mention that every Pokemon colored black should've had an added Dark-type.