As of 583 we have further confusion with the revelation that Komamura's grandfather is a a gigantic, non-anthropomorphic canine, who is apparently none-too-pleased at Komamura's former shame at hiding his appearance. We later learn that Komamura comes from a clan of werebeasts.
There's an animated short movie named Buta, in which the main character, an anthropomorphic pig, is deadly afraid of cats. The oddest thing about this is the fact he has a henchwoman who is an anthropomorphic cat and he never seems to mind her on the slightest.
In The Cat Returns, ordinary housecats are extremely spooked and agitated at the arrival of a parade from the Cat Kingdom, containing cats that, aside from walking on two legs and holding things, look exactly like normal cats. This is made funny when anthropomorphic tuxedo cats, bouncers, stomp around and bully the riffraff away.
Being that the Digital World and Real World are entirely separate entities, this is inevitable in pretty much every Digimon canon, with both animals and animal-inspired Digimon sort of coexisting. One of the best examples comes from Digimon Adventure, where Kari has both an actual pet cat, Meeko, and is partnered with Gatomon, a cat Digimon; the two don't appear to ever meet though. Also, while fish-based Digimon do exist, Gomamon's Marching Fishes attack appears to summon real fish, even in the Digital World.
In Eden's Bowy, Ms. Nyako, a humanoid catwoman, is absolutely shocked to hear a talking white leopard (secretly the goddess Enefea, who had been punished by her father, the god Lumezavia, to be trapped in such a form.)
Ms. Nyako: What?! The cat spoke?!
In Hyper Police, the main character Natsuki Sasahara is a cat girl who lives with several dozen cats. Likely subverted by the fact that she is half cat goddess; her mother is the Egyptian sun goddess Bastet.
One episode of Kirby of the Stars involved a colony of penguins on a motorized ice floe taking over Dream Land after their own home was destroyed. Wait a minute, isn't King Dedede also a penguin?note It should be noted that those same penguins appear as enemies in some of the Kirby games as it is. Though Escargo(o)n does call the Wandering Pengi "Your Majesty's relatives", at least in Japanese.
The anime frequently features non-sentient fish. One recurring character, Kine, is a talking fish. A late episode has a slightly disturbing scene where Kine tries talking to some of the main characters while they're fishing. He doesn't seem to understand why this is a bad time for a chat. Then they explain that he could end up as sushi if he sticks around, and he's naturally terrified. On that note, the episode in which Kine was introduced included a scene where Chef Kawasaki tried to cook him and feed him to a customer.
Escargo(o)n has been shown on various occasions to be less than happy about the fact that some people eat molluscs, including snails. Nobody else seems to have a problem with the idea, despite the existence of snail-people. At one point, Dedede even offers Escargon some of the shellfish that he's eating - Escargon refuses for obvious reasons.
It has been thoroughly pointed-out that the animal-characters on Nagasarete Airantou look nothing like the animals everywhere else in the world. Meimei makes costumes of the said real animals, drawn rather realistically for effect, that scare animal-characters of purportedly the same species.
In Naruto, there are talking dogs like Pakkun and non-talking dogs like Akamaru. The strange thing is that both seem to be of about the same intelligence (Akamaru can actually use Jutsu) but only one can speak the human tongue. Possibly justified in that Pakkun is a summoned animal (who all seem to talk, being mystical creatures and all) while Akamaru is just a normal dog. Well, normal aside from the fact that he's trained in ninjutsu.
One omake has Naruto lampshade Pakkun speaking (who apparently was taught by Kakashi to do so) to Kiba (who can understand Akamaru's barks). The latter confirms that Akamaru will eventually be able to speak human like the other dogs in his clan, but whether it comes naturally or with outside aid is left ambiguous. Akamaru then tries to speak to Naruto. His first words; Meow.
Very easily Hand Waved due to the nature of One Piece. This is slightly averted for all Zoan type Devil Fruit users, who are animal-humans, but is played fairly straight with Tony Tony Chopper the human-reindeer.
Some creatures are still of very questionable species, however, seeming to be neither human nor animal and yet not stated as Zoan-types either, such as Hamburg from the Foxy Pirates, who seems to be a Gorilla-man but is otherwise not shown to be a zoan-type user.
The Mink tribe plays with it a little, but generally manages to avoid it: Any animal with actual fur can have a mink, and they're an entirely separate species from humans (though they do think humans are some kind of furless monkey mink). The meat-eaters among them apparently eat any furless animals, as they don't have minks. While it includes reptiles and birds, as expected, it also includes hippos, which are mammals and would confuse the matter if "furless" wasn't the explicit thing. The part about birds can also be slightly confusing, depending on what "Big News" Morgans, who is introduced in a subsequent arc and could be best described as a bird mink if such a thing existed, turns out to be.
The intro to the Parappa The Rapper has Parappa giving flowers to his crush, Sunny Funny. Sunny is an anthropomorphic sunflower herself.
Averted in Porco Rosso, where the main character is human turned into an anthropomorphic pig, and therefore, has no problem with eating ham.
And of course, real life pigs often have no issue with eating pork either...
In an episode of Sonic X , Sonic runs into a normal hedgehog. Then again, Sonic comes from another dimension and looks absolutely nothing like a hedgehog...
In Suzy's Zoo: Daisuki! Witzy, there are two turtles named Teeter and Totter that are zoomorphic. However, the show is said to be set in the same universe as the main Suzy's Zoonote official artwork of Witzy meeting Suzy Ducken confirms this, where there's an anthropomorphic turtle named Corky.