In "Lisa On Ice", during Lisa's nightmare about failing gym:
Judge: I sentence you to a lifetime of horror on Monster Island! (aside) Don't worry, it's just a name. [Cut to Monster Island; Lisa and others are chased by lookalikes ofMothra, Rodan and Gamera] Lisa: He said it was just a name! Man: What he meant is that Monster Island is actually a peninsula.
Subverted in "'Scuse Me While I Miss The Sky", with the Deadly Meteor Shower; people are apprehensive about this name, until Lisa explains that it was named after its discoverer, Professor Artemis Deadly - who was killed in the shower of 1853.
And in "The Color Yellow," Bart learns that the Underground Railroad was neither underground nor a railroad, and wonders why they didn't call it "the Above-Ground Normal Road."
This exchange from the "Treehouse of Horror III" story "King Homer":
Carl: Hey, I hear we're going to Ape Island. Lenny: Yeah, to capture a giant ape. I wish we were going to Candy Apple Island. Charlie: Candy Apple Island? What do they got there? Carl: Apes, but they're not so big.
"22 Short Films About Springfield" actually has only 19 segments. Well, it would've been 20 if Professor Frink's segment hadn't been cut off by the end credits. Or, 17 segments if you counted Lisa's 3 segments as 1.
Lampshaded and Played for Laughs in "The PTA Disbands". When Springfield Elementary's teachers threaten to strike, a man horrifyingly yells "The PTA has disbanded!", and jumps out the nearby window, before Flanders explains that the PTA has not disbanded, prompting that man to jump back through the window, dusting himself off.
Fry: "Philip J. Fry, the Original Martian." Lies! Every word of it! He wasn't original, he wasn't a Martian, he wasn't Philip J. Fry, and since when is he a "The?" Bender: You're twice the "The" he ever was!
The Cave of Hopelessness. Named after Reginald Hopelessness, of course.
Who, in a similar gag to The Simpsons one above, was the first man to be eaten alive by the Tunneling Horror.
The episode "Fun on a Bun" is actually a big Tear Jerker.
One-time character Prof. Fisherprice Shpeekenshpell is actually based on another toy, a Mattel See 'n Say (also, the Speak & Spell was actually manufactured by Texas Instruments, not Fisher-Price).
South Park has the song "Kyle's Mom Is A Stupid Bitch In D Minor," which actually begins on a D-minor chord, but then immediately switches to a major key—nothing sung by Cartman is in a minor key. This might be a reference to "Singin' in the Rain in A-Flat" — which is actually in E-flat.
In the G1 episode "Enter the Nightbird", the character who needs help jumping up a cliff is the guy named Cliffjumper.
Bluestreak is silver, and not blue. Ironically, the Diaclone toy he was redecoed from was blue, and his packaging art showed him as being blue. Due to trademark problems, he was renamed "Silverstreak" in the 2000's, which fits better. But his thing is that he never shuts up; he talks a blue streak. "Silverstreak" just describes his color and implies that he's fast.
Transformers: Shattered Glass is a mirror universe story, where very few characters have changed names but nearly all have flipped personalities. This results in, among others, the dapper, cultured Abominus, the dashing, heroic Colonel Deathsaurus, Astrotrain, who doesn't turn into a train, Space Cowboy Bludgeon, and Whisper's No Indoor Voice. Sometimes, this gets a Hand Wave; Abominus named himself after a poem, and Whisper's name is apparently an Ironic Nickname.
Spongebob Squarepants: Neither the eponymous SpongeBob, nor his pants, are actually square. He and his pants are rectangular prisms composed entirely of rectangular faces. Also, Squidward is an octopus, not a squid (Taken a bit further that he has 6 tentacles, not 8).
Similar to Squidward above, a 1960s Hanna-Barbera character Squiddly Diddly is an octopus, in spite of his name.
In the Disney film The Great Mouse Detective, Padraic Ratigan actually ISN'T a rat; he's just a mouse drawn to look like a rat.
Phineas: (After Candace and various others start falling from a plane) Wow, dumb luck. And over the Sea of Razor Sharp Rock Spires too! The Others: AAAAAAAAAAAAAAHHHHHHHH! Phineas: Good thing it was so inappropriately named! (Candace and the others land on ground made of pillows.)
Flounder from The Little Mermaid is not a flounder (a flat gray fish that disguises itself as the bottom of the sea floor), but some sort of yellow tropical fish with blue stripes.
Similarly, Marlin from Finding Nemo is actually a clownfish like his son, Nemo. This was lampshaded about halfway through the film when Nigel the pelican tells Gill that Nemo's father shares his name with that of "a popular sport fish." Also, Dory is not a dory, she's a blue tang.
The Quack Pack version of Duckburg, unlike the one seen in DuckTales and in the comics, is actually not populated by ducks (or any anthropomorphic animal), with the sole exceptions being Donald, Daisy, Professor von Drake, and the nephews.
Also, Duckworth (Scrooge McDuck's butler), despite his name, is actually a dog.
From Teen Titans the H.I.V.E. Five actually had six members in their third appearance, as Kid Flash quickly noticed.
In My Little Pony: Friendship Is Magic, there is a place known as the Crystal Empire. It's actually a city-state within the kingdom of Equestria, whose head of state is a princess (albeit one implicitly lower ranked than the reigning Equestrian diarchy), rather than an empress. Back when it was actually independent, it was ruled by kings and queens rather than an emperor or empress.
The Sonic Boom episode, "The Sidekick" features Sonic going up against one of Eggman's robots, entitled "Burnbot". Said robot does not have any fire or chemical weapons, but claws instead. Sonic suggests using a name that isn't so misleading. Later in the episode, it is revealed that Eggman did take Sonic's advice by adding flamethrowers to Burnbot. Within the same episode, there's also the "incredibly dangerous, but inaccurately named" Mount Safety.
The Show Within a ShowBall Fondlers from Rick and Morty is actually an alternate dimensional version of The A-Team with a lizard man, a lady superhero, and a Mr. T lookalike with a girly haircut and has nothing to do with balls or the fondling thereof, with the only purpose of the title being a sexual innuendo.
A character in Danger Mouse was named Prof. Squawkencluck despite being a mole. Averted in the 2015 reboot, where the character is now a chicken.
The original Squawkencluck's name only made sense in his first appearance, where he did experiments on chickens.
EVE's job in WALL•E is to look for living plants on Earth, which is the one place she shouldn't be looking according to her name (Extraterrestrial Vegetation Evaluator).
Animated short The Street has nothing whatsoever to do with a street. It's about an old grandma dying, and how her family deals with it.