Sonic himself looks little like his animal namesake. His spikes look more like styled hair and he hardly has a snout. Instead, he has a jellybean-like nose that's close to face. Same goes for the other hedgehogs; Amy, Shadow, and Silver. Also, hedgehogs aren't blue, pink, black, or silver.
Knuckles is an echidna, but because his spikes look more like styled hair, he hardly has a snout, and has a jellybean like nose that's close to face, it wouldn't be too hard to mistake him for a "hedgehog".
Nack the Weasel doesn't look much like a weasel and in the Japanese version he is actually half wolf.
Jet the Hawk's green feathers and red markings around his eyes make him look more like a parrot than a hawk. Jason Griffith's voice for him doesn't help either.
Hell, most of anthro characters hardly resemble the animals they're supposed to be. Only a few are actually readily identifiable as what their name refers to them as. Tails is the one who looks most like his species; with Cream, Vanilla, and Vector also being easy to tell.
Chuchu from Kirby's Dream Land 3 is supposed to be an octopus, but looks more like a squid, or ghost, or... something. It's because she's a flapjack octopus, but even then...
Crash and Coco don't look much like bandicoots. Coco especially, since she lacks a long snout like her brother.
Tiny Tiger looks like some kind of big cat, but definitely not a Tasmanian Tiger. Real Tasmanian Tigers had light brown fur, stripes down their lower backs, and straight tails similar to dogs. Tiny is bright orange, has no stripes, and he has a distinctly lion-like tail, with a tuft of fur at the end. Crash of the Titans drastically redesigned him into being a standard Bengal Tiger, and he averts this trope in that game.
Dingodile has a crocodile tail, and his body is generally shaped like a crocodile as well, which means that the only resemblance he bares to an actual dingo is having fur and ears.
The Buzzy Beetle enemies (which are basically fireproof Koopa Troopas) from the Super Mario Bros. series games actually look more like hunchbacked, gray turtles than actual beetles. In fact, they actually look more like turtles than the Koopa Troopas, which are based on turtles!
Diglett and Dugtrio, despite being both called moles, don't actually look like moles at all! (for one thing, neither of them have visible bodies) Drilbur and Excadrill, however... Diglett and Dugtrio could actually be a Stealth Pun, as they bear more than a passing resemblance to the "moles" you hit in "whack-a-mole" games.
Sandshrew and Sandslash who are said to be mice, but they look more like armadillos or pangolins. Sandslash's Japanese name is Sandpan.
Caterpie is listed as Worm, but it's a caterpillar (as it appears in Japanese).
Blastoise evolves from two turtles, but his description puts him as "shellfish" (possibly because the cannon in his shell look like the tubes found in mussels; the Japanese one is just "Shell"). The same English and Japanese names apply to Kabuto (horseshoe crab) and Kabutops (a mix between the sea scorpion and the trilobite).
An interesting variation and double-subversion come from Rattata and Raticate. Originally, they were listed as rats in the games, but have since been retconned into being mice.
Snubbull and Granbull look nothing like fairies; they're clearly based on English Bulldogs. In Pokémon X and Y they were changed from being Normal types to the new Fairy types.
Raichu is said to be a mouse, but more strongly resembles a gerbil or possibly a jerboa.
Pikachu is said to be a mouse, it looks more like a rabbit with a zigzag tail.
Psyduck and Golduck are said to be ducks. Well, Psyduck kind of looks like a cartoony duck. Golduck, on the other hand, looks more like a platypus. Golduck is actually more based off of the Japanese YoukaiKappa.
Growlithe is said to be a puppy, but it has tiger stripes. Justified, in that Growlithe and Arcanine are loosely based off of the Shisa in Japanese folklore.
Weepinbell and Victreebel are said to be flycatchers. But are clearly pitcher plants.
Slowbro is said to be a hermit crab, but it looks more like a strange cross between a hippopotamus and a salamander with a shell on its tail (the shell is the only part that fits the name - and is possibly why in the original it's "Tenant"). Dwebble and Crustle on the other hand...
Scyther is said to be a mantis, but resembles a scythe-armed lizardman with bug wings and a small thorax in place of a tail.
Cyndaquil is also said to be a mouse, but more strongly resembles an echidna.
Wooper and Quagsire are said to be fish, but are closer in appearance to axolotls or mudpuppies.
Likewise, Mudkip, Swampert, and Marshtomp are also said to be fish, but more closely resemble salamanders.
Vigoroth is said to be a monkey, but it strongly resembles a sloth on steroids rather than any known species of monkey. Vigoroth's line, which are based on sloths, is a strange case, as its original form, Slakoth, does look like a sloth, but Vigoroth looks more like a mix of a sloth and some kind of monkey. Slaking looks like a giant sloth mixed with a gorilla.
Cradily is said to be a barnicle, but it looks more like a sea lily.
Bidoof is said to be a mouse, but it looks more like a gopher or a mountain beaver. Oddly enough, its evolution, Bibabarel is said to be a beaver and actually looks like one.
Torterra is said to be a tortoise, but it looks more like an ankylosaur.
Kricketot and Kricketune are said to be crickets. Though, Kricketot looks more like some sort of beetle and Kricketune looks like a mantis with a mustache.
Subverted with Snivy, Servine, and Serperior. While they are said to be snakes, they do have limbs (Snivy and Servine have both arms and legs while Serperior just has arm-like frills). Justified, in that prehistoric snakes did have limbs.
Tranquil is said to be a pigeon, and the Pokémon but looks more like a cross between a pheasant and a hawk.
Stunky and Skuntank are supposed to look like skunks, but they have cat heads instead. Also, Skuntank looks more like a honey badger than an actual skunk.
Shelmet is supposed to be a snail, but snails don't wear helmets. Or dress like ninjas.
Chespin is supposed to be a hedgehog, but he more closely resembles a rabbit or an otter.
Tyranitar's name would suggest a Tyrannosaurus rex, however it more closely resembles Godzilla than anything else note Who is himself supposed to be based (partially) on a T. rex while hardly resembling one . Tyrantrum finally brought a proper T. rex into the fold.
Zangoose is listed as a "cat ferret", and it actually kind of does look like a cat. But its name and hatred of Seviper clearly peg it as a mongoose, which it doesn't resemble so closely.
Despite its name, Pidgey more closely resembles a sparrow or a finch than a pigeon. While its evolutions, look more like birds of prey.
Beedrill is known as the "Poison Bee Pokémon", but it's actually based on the Asian Giant Hornet.
Magmar and its evolutions are particularly weird cases of this—design-wise, they look like, at best, like hadrosaurid dinosaurs and at worst, like something completely made up. What are they according to Word of God? Birds. More specifically, blue-footed boobies. Now to Nintendo's credit, this does explain why their Japanese names have the word "Boob" in them and it even explains their "magma" theme (blue-footed boobies are endemic to the Galapagos Islands, which are hot spots for volcanic activity), but would you really look at this◊ and believe that it was inspired by this◊?
Fire Leo from Viewtiful Joe, despite being a lion actually doesn't even look like a lion at all. Joe actually calls him a dog, but he hates being referred to as such.
The Pachycephalosaurus from the original looks more like a Prenocephale or a Stegoceras due to having a blunter snout.
The Chasmosaurus from the second game more closely resembles a Triceratops.
Ice Age has a wild boar which more closely resembles a warthog.
Also from Ice Age, the yeti has bird-like feet of a theropod dinosaur and three-fingered hands. While the creature still has status as a cryptid, most reports state it would have hands and feet no different than a hominind.
James Pond is claimed to be a cod, albeit that's mainly to have a "Robocod" pun in the second game. James is bright orange throughout, while real cods have a white underbelly and a dark green or grey topside.
Sash Lilac of Freedom Planet is supposed to be a dragon, but in actuality looks more like a purple cat-thing. It helps that the game had it's origins as a Sonic fangame, and still has a similar art style.
If it weren't for the title, you'd have no idea that the little people in blue robes with wild green hair in Lemmings were, in fact, Lemmings. As a Seldom-Seen Species you might even expect actual Lemmings, which are mouse-like animals, to look similar, or even not realize that Lemmings were a type of animal at all.
Infinity Mijinion from Megaman X 5 is supposed to be a water flea. He looks like a short fat man in a spacesuit.
Komasan from Yo-kai Watch is meant to be a Komainu (lion-dog) and has some Shiba Inu influences but he just comes off as a Cute Kitten and if anything looks like a panda.
Sheldon from Splatoon is allegedly a horseshoe crab, but he looks more like a generic yellow cartoon humanoid wearing a horseshoe crab shell as a helmet.
Swampy and the other alligators in Where's My Water? more closely resemble crocodiles since they have thinner jaws and the lower teeth sticking out of their mouths (with the exception of Allie, who only has her upper teeth visible like a real alligator).
Falco Lombardi from the Star Fox franchise is said to be a pheasant by Word of God, but looks more like a falcon with pheasant-like plumage. The fact that his first name is Falco doesn't help.
Krystal from the unreleased Nintendo 64Dinosaur Planet is meant to be a fox however she looks like some sort of big cat instead. When the game was changed to Star Fox Adventures she was redesigned to look more fox-like (and be Hotter and Sexier).