Arthur Read and his relatives are aardvarks, but aren't readily identifiable as such. Real aardvarks have giant noses that stick out. Arthur, D.W., and other Reads have no nose. Averted in the early books, in which Arthur's enormous nose is actually the driving force of the plot.
Notably, there was an old CBBC puppet mascot called Otis The Aardvark, who looked more like an aarvark than Arthur ever did. The original Arthur's nose points downward, whereas Otis' nose sticks straight out like that of a real aardvark.
Brain and the Tibble Twins are supposed to be bear cubs, but they look more like gophers than actual bears.
Prunella is supposed to be a rat (like Mr. Ratburn), but her ears and hair make her look more like a poodle.
Wendell T. Wolf from Taz-Mania is supposed to be a Tasmanian wolf (beige fur and a striped back), but he looks more like a miniature version of Wile E. Coyote with grey fur.
Jake from My Gym Partners A Monkey is supposed to be a spider monkey but, while obviously a primate of some kind, looks little like the actual species. Lampshaded in one episode that shows his family at the zoo at first appear to look correct but after the humans leave they remove disguises showing they actually look like Jake.
Daggett and Norbert from The Angry Beavers don't look an awful lot like beavers, even though they do have flat tails. This is constantly pointed out in the show, as most people assume that they are weasels.
The Tick owns a capybara named Speak (named because he once hallucinated it talking to him) who looks much more like some sort of mutant pug dog; in fact, the Tick was sure Speak was a dog until he took him to the vet.
The titular Aardvark from The Ant and the Aardvark doesn't look very much like an aardvark, having blue fur, a long snout more like that of an anteater's than an actual aardvark's, and long angularly bent ears.
Cyrill Sneer and his son Cedric on The Raccoons are suposed to be aardvarks, but have pink fur and snouts that bend down. The show's creator did this on purpose so kids don't think that real aardvarks are greedy industrialists.
Stitch himself is described as being a dog, but he actually looks more like a mutant koala instead, as pointed out by Nani about halfway through his film.
Though unlike other examples Stitch isn't actually intended by the creators to be a dog. Which is good considering his default form has six limbs, antennae, and dorsal spines.
An episode of Cyberchase involved The Hacker using a giant hamster in an exercise wheel as part of one of his evil plans to undermine the Mother Board and take over Cyberspace. However, for some reason the aforementioned hamster looked more like a capybara than an actual hamster.
Sherlock from Sweet Cuppin' Cakes is supposed to be a mix between a cow and a helicopter, but he looks like neither.
Rigby from Regular Show is supposed to be a raccoon, but for some reason he looks more like a brown coati (a South American relative to the raccoon) instead.
Margaret is supposedly a robin, but looks just like a male-colored cardinal.
And Eileen looks more like a midget human with three pointy toes on her feet and a tail than a mole.
That ostrich and possum in "Replaced". The ostrich looks like a duck. The possum...well, he may just be the technical "possum" (the one that lives in Australia).
Several characters of Rocko's Modern Life don't exactly look like the animal they are supposed to be. For example, the Chameleon Brothers look more like some kind of theropod dinosaur than actual chameleons.
The Giganotosaurus, Zuniceratops, Velociraptor, Eotyrannus, and Troodon from I'm A Dinosaur look more like Tyrannosaurus, Triceratops, Utahraptor, Tarbosaurus, and Coelophysis respectively.
The leopard seal from Pingu Dreams hardly looks like a real leopard seal and more closely resembles a walrus without tusks instead.
Mr. Bogus, as well as his younger cousin, Brattus, are supposed to be gremlins, but due to their yellow skin, it's indeterminate whether they actually are gremlins or just little people.
Horace Horsecollar is supposed to be a horse, but looks more like Goofy (whose species is ambiguous) than anything else.
Steggy from the Chip 'n Dale Rescue Rangers episode "Prehysterical Pet" is supposed to be an alien Stegosaurus, but he looks more like a lizard with backplates and a spiked tail instead.
Most of the My Little Pony: Friendship Is Magic characters just barely resemble ponies, instead looking more like mutated toy-breed dogs with cat ears. While male ponies have muzzles that have some semblance of a real horse's muzzle shape, female ponies have muzzles shaped more like that that of mouse lemurs and galagos (or bushbabies). However, this makes them lookadorable.
Louis from Foofur is supposed to be a bulldog, but while his face and ears are like those of a real bulldog, his big bulky body would suggest otherwise.
Sully from Danger Rangers is supposed to be a seal. However, since he's fully anthropmorphic, he has normal legs instead of tail-fins, thus making him look more like a tailless otter.
Sammy K. Ferret from The Real Ghostbusters episode "Stay Tooned" is supposedly a ferret, he looks more like a wolf or coyote.
The Megalodon from the episode "Play Them Ragtime Blues" looked more like a mosasaur instead.
Sam the Sloth from the Timon & Pumbaa episode "Hakuna Matata U." looks more like a bear-monkey thing than a sloth.
The sloth from the Jungle Cubs episodes "The Five Bananas" and "The Elephant Who Couldn't Say No" looks exactly like Sam. Considering the series supposedly sets in Asia one wonders why they couldn't have used a slow loris instead.
The characters in Out There are human (by extension of background elements depicting humans and referring to humans as themselves) but they don't look too human at all, in fact most are fairly ambiguous in terms of species and the lead character Chad and his family look nothing like the others, instead being less ambiguous and looking more like very hairy rodents but still of indeterminate species and considered as part of the same species as the rest: "human".
The characters in Thundercats are meant to be humanoid cats but they just look like oddly colored humans with Anime Hair. Averted more in the 2011 reboot, where they make a better attempt at having them act and look cat-like.
Although mutated from ordinary turtles into the crime-fighting Teenage Mutant Ninja Turtles they are today, Leonardo, Michelangelo, Donatello and Raphael have little to no resemblance towards any real world turtle species other than their nondescript shells, looking more like green-skinned, humanoids with three-fingered hands. This despite the fact that most turtles (besides sea turtles) have five claws.
'Super Friends'' 1973-74 episode "Dr. Pelagian's War". The title character sends three marine creatures to attack Superman and Aquaman. Both characters call the creatures "whales" (and Superman says "killer whales") but it's blatantly obvious that they're actually large sharks.
In "The Devil and Daniel Mouse" the devil's associate Weez Weezel looks more like a wolf or coyote than a weasel.
Zoe from Littlest Pet Shop (2012) doesn't really look like a Cavalier. She looks more like a purple poodle with less curly fur.
Preston from Wallace & Gromit: A Close Shave is supposed to be a bulldog, but he is not identifiable as such. Although it may be justified in that he is a robot.
The eponymous Fat Dog Mendoza doesn't look very dog-like. He's orange, with a spherical body, four stubby legs, a long flexible tail and a vaguely human face that covers half the front of his body.
Antoine from Sonic Sat AM is one of these. This was even called out in a reader's letter in the Archie comic. It was established a while ago that he's a coyote. But for years (pre-Internet), the same question was asked as to what species Sally was, until she was established as a squirrel-chipmunk hybrid. Or a ground squirrel. Or a ground squirrel/chipmunk hybrid. We think.
The crocodiles from the Disney classic short "Pluto at the Zoo" look more like gharials in that they have much thinner snouts.