Bugs Bunny used to look more like a rabbit/hare in his early days, but Art Evolution made him the same size as a human and with much longer legs.
The Tasmanian Devil and the Tasmanian She-Devil are brown furred and look nothing like real Tasmanian Devils, which have black fur.
The Roadrunner also looks nothing like its real-world counterpart. Roadrunners aren't bright purple/blue nor are they the same size as a coyote.
Hippety Hopper, the baby kangaroo that Sylvester always mistakes for a giant mouse. In Sylvester's defense Hippety does look far more like a giant mouse than an actual kangaroo.
Yoyo Dodo basically looks like a drinking bird covered in a grass tunic.
Batty, the bat in the cartoon, "The Brave Little Bat," looks nothing like a bat, and looks like a mouse with wings instead.
Henery Hawk doesn't look that much like a hawk.
Rare human examples: Bosko and his girlfriend Honey are supposed to be blackface-looking African-American human characters, but they don't really read as such. They look more like ambiguous-looking chimpanzees or bonobos instead.
Dizzy Devil (the purple Tasmanian devil), Little Beeper (the red roadrunner), and Gogo Dodo from Tiny Toon Adventures inherit the non-resemblance of their forebears.
Shirley the Loon looks more like a white duck like those in Carl Barks' duck comics save for a thicker bill, than like any loon.
One of the episodes, "Who Bopped Bugs Bunny?", involved Babs and Buster trying to solve Bugs Bunny's mysterious disappearance. In the end the culprit is revealed to be Sappy Stanley, an elephant who competed and lost against Bugs Bunny in a parody of the Academy Awards. Although he talks through his mouth depending on his mood, most of the time Stanley speaks straight from his trunk (complete with mouth), making him look more like an anteater than an elephant.
Bonkers: Bonkers D. Bobcat hardly looks like a real bobcat; his tail is long rather than a stub, his snout is long like a dog's, and his ears are so thin and long they're almost like antenna. At least he has downward-facing cheek tufts.
Bungo from Jungle Junction is said to be a "bunny", but, rabbits don't have long striped tails.
Who Who the ring tailed lemur from the Animaniacs episode, "Back In Style" hardly looks like a real ring tailed lemur and looks vaguely like a red panda instead.
Calhoun Capybara from the same episode actually looks more like a yellow wombat than an actual capybara.
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 aardvark than Arthur ever did. The original Arthur's nose points downward, whereas Otis' nose sticks straight out like that of a real aardvark. Otis himself even commented on this, opining that Arthur looked more like a hamster.
Brain and the Tibble Twins are supposed to be bear cubs, but they look more like gophers than actual bears.
Sue Ellen and Jenna are cats, which is why they both have little button noses and whiskers...wait...
Prunella is supposed to be a rat (like Mr. Ratburn), but her ears and hair make her look more like a poodle. Due to Flip-Flop of God it's unclear though. She may actually be a poodle, since Marc Brown Studios' Facebook page says she is. Oddly enough, she looks more like a rat in Brown's books, sporting a pair of sharp teeth that disappeared when she made the transition to television. The official Arthur website says she's a rat. It seems all we can say for sure is that Prunella looks confusing.
Muffy and Francine are monkeys but they just look like humans. In the early books they had muzzles but in the cartoon their fur is one tone all over.
The only exception seems to be Buster, who is said to be a rabbit and actually looks like one.
P.J., Pete's son from Goof Troop, A Goofy Movie, and An Extremely Goofy Movie, is supposed to be a cat, but in all his appearances, he looked more like and was treated like a Dogface with pointy ears instead.
Chip and Skip from Camp Lazlo are supposed to be dung beetles, but look more like purple things. Ping-Pong and Dave are supposed to be loons, but they look more like ostriches. And, for some reason, the Lemming brothers look more like green frogs with ears than well....lemmings.
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 Partner's 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 angular bent ears.
Even more so in Pink Panther and Pals. This time the Aardvark's snout is curved upwards like an elephant's and his tail is shortened.
Cyril Sneer and his son Cedric on The Raccoons are supposed 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.
SpongeBob looks more like an artificial dish sponge than an actual sponge, even though he is supposed to be the latter.
Squidward is actually an octopus despite his name. He lacks two tentacles because it was seen as a burden to animate.
Actually, since both octopi and squids exist in the show and look different to him... we don't know what the hell he is.
Austin from The Backyardigans is a kangaroo, but looks more like he's half aardvark and half cat.
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 is supposed to be a North American raccoon, but strongly resembles a Crab Eating Raccoon or a Coati, both of which only have a short brown layer of fur, and more slender bodies. Crab Eating Raccoons are native to Costa Rica and South America and Coatis can be found in the Southwest US including Southern California. Rigby's lack of a proper face mask has been explained by the fact that he has huge cartoony eyes, and is occasionally shown blinking where he has black eyelids. This is consistent with his more humanoid looking brother Don too. Rigby's lack of resemblance to his real life counterpart has been Played for Laughs on multiple occasions - he comments on the black circles around his eyes as being 'his thing', when he and Mordecai encounter realistic animal versions of themselves Rigby is drawn as a standard gray and black raccoon (present on a comic cover too), and in an early episode, one of the enemies says to him 'what are you supposed to be?'.
Margaret is supposedly a robin, but has a coloration and crest of a male cardinal.
Eileen is supposed to be a mole, but for some reason, has a human face!
The ostrich and possum in "Replaced" look more like a combless chicken and a stripeless numbat, respectively.
The hedgehog from the prequel Thanksgiving special "Meet Bigpaw" looks more like a porcupine than a real hedgehog. Conversely, Mr. Porcupine from the episode "Raid on Fort Grizzly" looks more like a hedgehog than a porcupine.
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.
All of the fish from Fish Hooks look like finger puppets with a few fins.
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.
Justified in that gremlins don't have a stablished look.
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 bizarre dragon creature 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.
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".
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.
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 SatAM 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". Their thin snouts indicate they could be freshwater crocodiles or slender-snouted crocodiles, but they are much larger than both species.
SwaySway and Buhdeuce from Bread Winners are identified as ducks but they look like frogs with noodle arms and orange mouths.
The emu from the Mickey Mouse short "Mickey Down Under" more closely resembles an African ostrich.
Belfry from Filmation's Ghostbusters is a bat, however he looks like a fanged pig with wings.
The main trio of Mega Babies look more like colored monsters or space aliens than human beings.
Yehudi the chameleon in the 1944 Wartime Cartoon "Camouflage," looks more like a generic green and white lizard than any chameleon.
Word of God stated Larry is a rock-man, but looks more like he's made of origami.
Ocho doesn't look much like a spider: he only has two human-like eyes, a single body segment, and four legs. Justified as he's originally a video game character in-universe.
Darwin's rounded face and tailfin make him more resembles an orange blobfish than a goldfish.
Penny is a shelled peanut with antlers, but her first season design only has one chamber, making her look more like a coconut or walnut. Her design from the second season on has two chambers.
Miss Simian is supposed to some kind of primate, but her specific combination of features don't match any real species. She most closely resembles a chimpanzee with a tail.
The protagonists of Catscratch are cats however Mr Blik and Waffle barely resemble cats. They're bipedal and have skinny, long ears. They resemble rabbits more than cats, especially Waffles with his floppy ones.