In the original games, the main characters are anthropomorphic animals (albeit oddly colored) who save not-so-big 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.
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.
Let's not forget that in the games, the western animated cartoon series, and the comics based on them, Sonic's favorite food was chili dogs. Now where in the hell does the meat come from?
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 three of these species are also the species of members of the cast.
In the Lost Jungle level of Sonic Heroes, you can encounter a giant non-anthropomorphic crocodile. 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 crocodile. This may be a weak effort to avoid Furry Confusion.
Parodied in a skit from the Sonic Shorts series of fan-made skits. Sonic and his friends, who are all staying at the Thorndyke residence, are fed different kinds of foods, all of which apply to the diets that their species have in real life. Knuckles is given non-anthro (but still talking) ants, and Tails is given a non-anthro, cooked rabbit. Cream, who is sitting next to Tails at the time, starts crying, and runs out of the room.
Parodied in yet another Sonic fan video, where a non-anthro hedgehog approaches Sonic with another non-anthro hedgehog who was run over by a car. The living non-anthro says to Sonic, "Avenge him, Sonic! Avenge your brethren's death!"
Tauren (Minotaurs) in World of Warcraft are able to raise horses, pigs... and cattle.
While there are certainly non-anthropomorphic cattle livestock in the game, the Tauren don't keep any. Tauren do, however, raise Kodo, which are kind of like rhinoceri. Cows raising animals as mounts, meat and milk producers has to be even more bizarre than if they were just raising cows.
A Tauren Pirate (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.
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 was 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.
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.
Perfect World features the Untamed, whose men are Anthros and whose women are Petting Zoo People and capable of physically turning into a tiger and fox, respectively. The God of the Perfect World is also a Anthro Panda. Despite this, the Untamed raise pet cats, hens, and dogs. Even more strangely, there are (things that look like) pack animals that are apparently sentient and have their own complex language — and these pack animals can pick up English if they travel enough, and most do. It gets even more bizarre with the various quests that treat entirely non-anthro and non-speaking monsters as highly sentient, and when anthro and communicative monsters drop valuable types of Meat.
In Animal Crossing 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 neighbors 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.
In Wild World, (somewhat disturbingly) one of the hats you can wear is a cow/bull skull (complete with horns). Now if you'll excuse me, I'm off to visit my cow/bull neighbour.
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.
In the Breath of Fire games, your entire party by and large consists of full anthros and petting zoo people, 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 where your dogman friend objects to a pig being cooked, but that's because he was being paid to retrieve it...)
Partially lampshaded in IV, at least per the artbook.note All humanoids in the game, with the exception of the PabPab, were adopted by a specific god and changed as a result of their adoption/connection. It's still squicky in a totemic sense, though.
In Pokémon, pretty much all of the animals are replaced with Pokémon. Fish and insects have appeared (despite there being an entire type devoted to bug Pokémon), and there are allusions to animals like dogs.
Really, the confusion isn't so much non-Pokemon dogs appearing with Pokemon ones, but more of "if all animals (and many non-animals) are Pokemon then where are the myriad insects integral to decomposition?" and similar questions since what with the smallest Pokemon still being about 4 inches, many important roles in an ecosystem must be carried out by something that isn't a Pokemon, despite there not being much reference if any to non-Pokemon animals.
Animals do get referenced several times but they never appear within the games. This could be do to graphical limits - that they don't need to be seen so they don't appear in sprite form but are supposed to exist - or they may just not exist within the areas the games take place.
Thanks to Grass-type Pokémon, you can even run into Plant Confusion. Granted, some just resemble animals that have plant-like pieces — there are real-world animals like that (for mimicry purposes). But think about it when you harvest a berry tree and give one of those berries to an ambulatory coconut tree... Yeah, that's weird.
How about Leafy Confusion? The WiiWare game 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.
Neatly averted in Beyond Good & Evil. Yes, there are goat-people, shark-people, rhinoceros-people, et cetera, but your camera explicitly states their species as "[genus] Sapiens"; the goat-people, for instance, are Capra Sapiens.
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.
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.
Averted on 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. Oh, and there's anthropomorphic insects, but they behave and reproduce like real-world bees. On the other hand, this is only in Furcadia canon — and anyone who's been there knows that hardly anyone plays by canon rules...
The Super Mario Bros. series games actually feature both anthopomorphic mushroom people and nonanthropormorphic mushrooms as power-ups.
With the added confusion that the power-up mushrooms (and a whole bunch of other stuff) still have eyes.
Okami: 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.
The JumpStart 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 1998), the main character is an antropomorphic rabbit named Mr. Hopsalot, and non-antro 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 (aka 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 featured the JumpStart anthro animals...taking care of pets. That were sometimes the same species as themselves. Just look at the cover◊ - Frankie the dog is holding a non-anthro dog in his hands! Or are they paws? Hmmm...
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.
The 2009 Wii game JumpStart Pet Rescue is another example.
In Stage 4 of Pa Rappa The Rapper, Cheap Cheap Chicken teaches PaRappa how to make a seafood cake. The first step? "Crack-crack-crack the egg into the bowl!" Yes, that's right, a chicken cracking open an egg (sure, it's an unfertilized egg, but still).