AMC Squad: One of the main characters, Kagura, owns a pet cat that she keeps in her quarters in the AMC Base. However, the same game has Snowfall, an anthropomorphic cat, who can visit her quarters and pet Kagura's cat. Neither the cat nor Snowfall seem to notice anything odd about this.
There are a few frogs and octopi among the various anthropomorphic animals who can move into your village, yet you can also catch non-anthro frogs and octopi while fishing. It gets more than a little unsettling when one of your neighbours asks you go catch a member of his or her own species... then keeps it in a tank in their home, or, worse, eats it once you present it to them. Not to mention the caged-bird furniture item that your bird friends will graciously accept and display in their house, or the hamster cage that hamster friends are fine with having in their homes or receiving as a gift from you, or the doghouse for dog villagers.
In Wild World, New Leaf and New Horizons, one of the hats you can wear is the "cow bone" — a bovine skull, complete with horns. Now if you'll excuse me, I'm off to visit my cow/bull neighbor.
In some games, it's actually possible for a cow villager to give you a cow skull as a present.
The fossils in the museum are all strictly non-anthropomorphic and overall very realistic, accounting for graphics. This includes the mammoth skeleton, which is quadrupedal and about four times as tall as your character. Tucker, the mammoth villager, is a humanoid cartoon animal same as everyone else and no taller than any of his neighbors.
In New Leaf, villagers will occasionally ask what kind of pet you think they'd like or what kind of animal you think they are most like. The species they actually are is a selectable option for both questions. The other options are species based on NPC characters.
New Horizonshangs a couple of lampshades. The museum's fossil section is themed around prehistoric evolution, with the Cenozoic room showing the existence of the various animal villagers as a massive case of convergent evolution. Also, if your villager catches a frog while fishing, they'll comment:
I caught a frog! Or it's a new neighbor... and I have some apologizing to do.
Arknights: The various races of Terra all incorporate Animal Motifs as a part of the Little Bit Beastly humans or downright anthro Beast Man, such as the Aslan race being lions and the Liberi race being various bird species. Non-anthro/humanoid animals frequently appear in an Operator's Elite 2 CG to reflect their respective Animal Motifs, such as Gavial (a crocodile), Skadi (an orca), or Zima (a bear).
Aviary Attorney takes place in a World of Funny Animals, but there are non-anthropomorphic animals around as well (though we don't directly see them). A kingfisher with a rod and line catches fish, riding horses is a thing (one character carries around a riding crop, and another character has statues of horses — not horse people, but actual horses — in his garden) although there's a donkey librarian around, and there are apparently edible and people versions of chickens and pigs.
Parodied in Barkley, Shut Up and Jam: Gaiden during Barkley and his companions' trip through the sewers of Neo New York when they come across a settlement of people who have undergone Magic Plastic Surgery that made them into anthropomorphic animals. They also come across a normal-looking dog, but another person says it's just a "furry" being in character.
How about Leafy Confusion? Bonsai Barber has a cast made up of giant sentient fruits and vegetables (and a cactus), but while a number of the characters are fruit, they can also grow fruit (apples) on their branches as well. To make matters weirder, you also have in your shop, in a position of prominent display, an ordinary potted plant "named" Prunella.
Breath of Fire: Your entire party by and large consists of full anthros, yet no one complains or even seems to think about it when you happily mow down, hunt, or fish their mundane, quadrupedal or legless counterparts, or use and abuse pack animals and pets. (Well, there is one scene in Breath of Fire II in which your dogman friend objects to a pig being cooked, but that's because he was being paid to retrieve it...)
Campfire Cat Cafe & Snack Bar: Fish and lobsters are used in some dishes... but one of the special NPCs is an anthropomorphic manta ray.
Cartoon Network Racing features the anthropomorphic Cow and Chicken as playable drivers but also features realistic, non-sapient cows and chickens on Farmed and Dangerous, the first track of the game.
In Dust: An Elysian Tail, you can often find little rabbits hopping about in some of the early levels. Then you encounter civilization... and there are quite a few rabbit NPCs wandering around.
Dusty Revenge and its prequel Dusty Raging Fist are set in a Western-inspired world, albeit one populated by andromorphic animals. While the game has rodent-inspired enemies like Rat Men, humanoid moles and badgers, the forest levels have non-anthro squirrels, and while the original game has Frog Men enemies, the prequel has non-anthro, normal frogs.
Eastshade is populated by multiple Funny Animal types — deer-folk, bear-folk, owl-folk, ape-folk and raccoon-folk — along with non-anthropomorphic domestic animals (cats, chickens, cattle, sheep). There's also references to elk and bears in NPC dialogue, and a wild owl you can encounter yourself (although the latter doesn't resemble the type of owl that the owl-folk do).
Electronic Popple is set inside a CPU where microchips, computer viruses, software and assorted programs are alive and sentient, and yet there are areas containing control panels and wiring that seemingly runs on non-sentient programs. Unless, of course, the interiors of those panels contain even smaller living software...
Played with in Final Fantasy XIV. In their end of the Monster Hunter: World collaboration, your Warrior of Light meets a Felyne, a creature that is essentially a large cat with opposable thumbs and the ability to walk bipedally. One of your character's possible reactions to meeting them is to express amazement at a talking cat, even if they happen to be a Miqo'te or a Hrothgar, in which case the Felyne will actually call them out on it.
Fashionable Feline: Oh, that's rich coming from you. Or have you not looked in a mirror lately?
Averted in Furcadia. The only anthropomorphic animals are mammals and lizard-like wyrmmes. Mammals can interbreed and create either hybrids, offspring that resemble a parent, or offspring that resemble one parent, and non-anthropomorphic animals are all birds. There are also anthropomorphic insects, but they behave and reproduce like real-world bees. On the other hand, this is only in canon — and anyone who's been there knows that hardly anyone plays by canon rules...
Hatoful Boyfriend has various species of birds as fully realized members of society, from pigeons to quails to partridges and more. One of the school activities is "birdwatching", and chicken is on the menu completely unquestioned. Later in the game you learn that the bird characters are Uplifted Animals. The virus responsible, Carneades, uplifted pigeons first and other species are affected more slowly, so some are still animals and some species are acclimating to being civilized. Summer swallows being small and fed by their parents for much longer than usual is taken as grounds to speculate that they're changing and maybe all birds will change. Since Carneades was developed by humans to annihilate all bird life but Went Horribly Wrong, they may have designed it to not affect livestock.
Island Saver: Bankimals are all non-anthropomorphic but there are anthropomorphic animal characters in the game like Bucky the Mule and Pigby.
The Jump Start series of edutainment games for children has several examples (and manages to never hang a lampshade on any one of them):
In both versions of JumpStart Kindergarten (1994 and 1997), the main character is an anthropomorphic rabbit named Mr. Hopsalot, and non-anthro rabbits also appear in the very same game.
JumpStart Around the World, a game which used to be included as a bonus disc with the Preschool - 2nd Grade titles (with a slightly different version for each grade) included at least two examples. In the 2nd Grade version, when you go to Brazil, there's a "photo" of your travels that depicts the anthropomorphic C.J. Frog and a lot of non-anthro tropical frogs clustered around his feet and even sitting on his head. In the Preschool version, taking a trip to Australia will yield a short video that includes Kisha Koala holding a non-anthro koala in her arms.
In JumpStart Animal Adventures (a.k.a. JumpStart Animal Field Trip), the main character is C.J. Frog, but the game also features a non-anthro (but talking) frog in the Rainforest section.
JumpStart Advanced Preschool features the JumpStart anthro animals... taking care of pets that were sometimes the same species as themselves. Even the cover◊ shows Frankie the dog holding a non-anthro dog in his hands (paws?).
Pretty much any time when a JumpStart game featuring animal characters also teaches zoology, this is bound to happen. For example, JumpStart Advanced 1st Grade taught just a little zoology, featuring a game in which you sometimes had to guide blimps labeled with pictures of animals to the classes to which they belong. Again, just like in JumpStart Kindergarten, the game is hosted by Hopsalot, but sometimes the blimps depict non-anthro rabbits - and other creatures that also appear as anthros in the game.
The trend continues. In the JumpStart.com MMOG, the user can adopt pets (styled as "petz") of all sorts of species, such as dogs, rabbits, and elephants...despite the presence of such characters as Frankie, Hopsalot (aka Hops), and Eleanor.
My Little Pony (Gameloft): In "A Mistmane New Year", the Mane Six are partnered with other creatures as dance partners, most of whom are Civilized Animals like themselves. Pinkie Pie is partnered with a monkey and spends some time telling him about a story, only for Trixie to inform her that he appears to just be "a regular monkey".
Trixie: Uh... Pinkie? I think that's just a regular monkey. Like... not the sentient kind? I'm sure he likes you, but I don't know if he understands... you know... any of that. Pinkie Pie: Really?! Aw, nuts... I thought he was just a really good listener!
Mae from Night in the Woods is a talking, humanoid cat, yet one of her neighbors has a normal pet cat. One of her (also humanoid feline) grandfather's stories features a talking cat as a magical, fantastical element. Likewise, the bird-based characters in the game walk right beside normal pigeons.
Ōkami: Sasa Sanctuary is staffed by anthropomorphic pseudo-Yakuza sparrows. You can find (and feed) non-anthropomorphic sparrows throughout the game, including just outside the Sanctuary.
In Stage 4, PaRappa is taught by Cheap Cheap Chicken how to make a seafood cake. The first step is to "Crack-crack-crack the egg into the bowl!" (sure, it's an unfertilized egg and chickens can easily be taught to find eggs delicious, but still).
In PaRappa the Rapper 2, Parappa's household contains a non-anthropomorphic domestic cat, even though his friend Katy is a cat.
Long after Pokémon completed its Earth Drift, Corsola (a lump of coral with a face) can be found in the same habitats as realistic-looking corals in games such as New Pokémon Snap.
The Przygody Reksia games center around a World of Funny Animals, but there are also non-anthropomorphic animals that have civilized counterparts. There are many anthropomorphic chickens in the series, including the Inventor Rooster and Korneliusz, but most of the hens that were kidnapped by the UFOs in the second game, two of which are the sisters of the aforementioned roosters, are non-sapient.
Something of an Elephant in the Living Room in the Quest for Glory series. Most of the non-human races are "evolved" animals like Katta (anthropomorphic cats) and Liontaurs (like centaurs, but with lions); however, regular cats and lions still show up in the series. Of course, Word of God says that the fantastic races exist because of an explosion of magic in the backstory, so the situation with them may be akin to the one between humans and apes.
She Likes You Alotl: Farelie is a humanoid axolotl, but the alligators and frogs appear to be normal animals.
In Shepherd's Crossing, your Exposition Fairy is a talking duck named Brammy/Brummy. However, you can also raise normal, non-talking ducks for eggs, feathers, and meat. The second game acknowledges this by having Brummy get very nervous when one of your neighbors shows you how to snap a goose's neck. That said, he also happily eats ham and sausage.
The Sly Cooper series of games takes place in a universe populated almost entirely by anthropomorphic animals. However, the second game features "real" bears and elephants, and the third game contains a "real" wolf. In both cases, the protagonists have to take advantage of their normal animal behavior.
A boss in the first game is an anthropomorphic alligator named Mz. Ruby. In the third game, there's a task that involves a non-anthropomorphic alligator and the team never questions this.
Sly 1 also features a leashed "real" dog enemies while the other dog enemies in the stage are anthro.
In Sly 2, Murray needs a disguise to enter an RC Combat match, so he puts on a stuffed moose head . . . that looks just like all the moose people walking around the building.
Also in Sly 2, the guards in Episode 1 are anthro rats, but in one of the missions in Episode 2, non-anthro rats are mentioned as scurrying away and scaring the elephants when you crawl into an area.
In the original games, the main characters are anthropomorphic animals (albeit oddly colored) who save smaller, less anthropomorphic animals from the clutches of Dr. Ivo "Eggman" Robotnik. This is especially weird in the Sonic Adventure games, where the playable characters can actually collect the non-anthropomorphs and give them to the Virtual Pet-like Chao. In this game, the animal friends are treated as Nearly Normal Animals instead of Partially Civilized Animals like in previous titles.
Some of the animals that can be rescued in Sonic Adventure include ordinary, non-anthropomorphic bats, rabbits, and swallows. Rouge, Cream, and Wave are respectively, an anthropomorphic bat, rabbit, and swallow. And while those characters weren't introduced until later games, the remake of Sonic Adventure has Cream make a few small cameos, with the animal list unchanged.
Sonic Adventure 2 takes the cake, as it has three different kinds of bats: the anthropomorphic Rouge (who is in fact more anthropomorphic than other characters), the cartoonish bats that raise your Chao's stats, and actual real-life bats flying around in the level "Death Chamber".
In the Lost Jungle level of Sonic Heroes, you can encounter a giant non-anthropomorphic alligator. If you play as Team Chaotix, one of your characters is Vector, an anthropomorphic crocodile. If you play Lost Jungle as Team Chaotix, you take an alternate route where you do not run into the giant alligator.
In Sonic Chronicles: The Dark Brotherhood, there are non-anthropomorphic animals that are common enemies. They include wasps, armadillos, boars, hawks, and millipedes. Note that threenote well, depending on how close you consider wasps and bees to be, though it's still weird regardless of these species are also the species of members of the cast.
In Sonic and the Black Knight, some of the items you can identify include bat's fangs and rabbit's tails.
Despite not actually featuring any real animals, Spore has occasionally fallen into this. Owing to the randomly generated wildlife, it's entirely possible that a nearby nest of creatures may actually be members of your own species... and you can kill and eat them. Granted, this game is meant to simulate evolution, and real animals definitely aren't immune to this either.
Justified; the world is populated by Standard Fantasy Races with the notable absence of humans. All Beastfolk are the same species regardless of appearance.
At a bakery, the anthro fox Melody explains is able to eat chocolate just fine, since it's only toxic to "regular canids, not beastfolk".
The games feature both anthropomorphic mushroom people and non-anthropomorphic mushrooms as power-ups. Adding to confusion: the power-up mushrooms (and a whole bunch of other stuff) have eyes.
This also applied to most of the species in the series based on real world animals. While all penguins and primates in the series are anthropomorphic, many others have both anthropomorphic and non-anthropomorphic members, sometimes even in the same game. Paper Mario: The Thousand-Year Door features both an anthropomorphic pig and characters who are cursed into normal pigs, for example; while WarioWare features both an anthropomorphic dog (Dribble) and a non-anthropomorphic but magical dog (Shadow), and there are also anthropomorphic dogs in Paper Mario known as Doogans.
Super Mario Odyssey introduces a forest full of "wild Goombas". This is despite Goombas historically being treated as sapient people, not animals.
Super Smash Bros. features anthropomorphic characters fighting animals that are cartoony at best. Granted, they're all from different video games, but it still feels kind of weird. Lampshaded by Wolf's Super Smash Bros. Ultimatecharacter video where he, an anthropomorphic wolf, plays fetch with the Duck Hunt dog, a... dog.
In Syrup and the Ultimate Sweet, Syrup and Butterscotch befriend a Little Bit Beastly wolf girl named Treat, and later get attacked by a pack of "real" wolves. While the game itself doesn't provide an explanation on this, the Lonely Wolf Treat series reveals that the animals in NomnomNami's universe are able to shapeshift between humanoid and beast form at will, and that wolves are known to change into their beast form when hunting.
An NPC in Snowdin is a rabbit woman who is seen with a non-anthropomorphic rabbit on a leash. A nearby NPC remarks on how odd the situation is. It turns out that the smaller rabbit is actually the rabbit woman's little brother.
Muffet is a Cute Monster Girl spider who lives in a nest full of Nearly Normal Animal spiders and... whatever her pet is. This does not stop her from making cider, donuts, and croissants out of her crushed-up kin.
The dogs from the game. Dogamy and Dogaressa, as well as Doggo, are all anthropomorphic, although they show dog-like behavior occasionally, and speak English. The Greater Dog and Lesser Dog are much less anthropomorphic, and do not speak. The Annoying Dog has little if any humanoid traits aside from a mischievous sense of humor, and speaks only in a joke ending.
A TaurenPirate (yes, he's as awesome as he sounds) has a price put on his head, and invokes the trope by sending a cow's head in place of his own. Seahorn suggests most Tauren are offended by people pointing out the similarity, while he finds it amusing.
Worgen involve this trope on a gameplay-level. The ones found in the game up until Cataclysm were all ferals, considered basically dangerous animals, and could be skinnable by players. Then Cataclysm added playable worgen, who only differs from the other ones by retaining their sentience.
◊ shows Frankie the dog holding a non-anthro dog in his hands (paws?).
