The Adventures of Captain Alatriste - The titular character Diego Alatriste is not a military Captain -nor even an officer- but in the story, he's working as a sword-for-hire under the monniker of "Captain" Alatriste. He is later recruited and promoted.
The Analects of Confucius aren't analects, and the Master's name wasn't really Confucius either.
In Anansi Boys, Fat Charlie is not, nor was ever fat. Between ages ten and fourteen he was a pudgy kid, but that was it. Unfortunately, while he lost weight, he could never shake the nickname because his father, Anansi, gave it to him.
Flann O'Brien loved doing this: The tiny Shannon River islet of Swim-two-Birds is mentioned exactly once in passing in "At Swim-Two-Birds".
The novel Breaking Smith's Quarterhorse would seem, from the title, to mostly revolve around a man named Smith, who has a quarterhorse in need of breaking. Smith is referred to in one line; the horse doesn't even get that. The book is actually about... not much, really.
Charlie and the Chocolate Factory: While the titular factory does make a lot of chocolate, it also makes many products that don't use chocolate, so it's not merely a chocolate factory, it's a candy factory.
In Harry Harrison's Deathworld 3, the planet Felicity (meaning "bliss" or "happiness") does indeed contain rich mineral resources (if that is your idea of bliss), but it was named before the galactic community realized that it's full of hordes of nomadic barbarians who absolutely hate permanent structures and will kill anyone who isn't a nomad. That also includes mining equipment.
The title of Return fo Deathworld (co-authored by Ant Skalandis and never published in English) is misleading in that no one has actually left Deathworld to return to it. The title apparently refers to the reader.
In Lords and Ladies, mention is made of the Carter family, who named their daughters after virtues and their sons after vices. They turned out to be non-indicative: Charity Carter grew up to be greedy and Prudence Carter wound up the mother of fourteen kids, while Anger Carter is known for being even-tempered and Bestiality Carter is known for being kind to animals.
In Men at Arms one of the city's most famous landmarks is the Colossus of Morpork. Unfortunately, since it was designed by the Giftedly Bad architect and inventor "Bloody Stupid" Johnson, the "Colossus" fits in a small cardboard box padded with cotton.
Dante's The Divine Comedy, the old definition of "comedy" is being used, namely a story with a happy ending, since at the end of the story Dante visits Heaven and meets God. The word "Divine" is a straight example, being a comment meaning inspired by God on the merit of the work. Dante originally just called it Comedy, and Boccaccio added the adjective.
In the Dragaera series, the titles of "Lord of the Keys" and "Lady of the Chairs" do not change based on the gender of the titleholder.
A halfway example in The Dresden Files with the Corpsetaker, who while as a necromancer could be considered someone who takes corpses, is mostly known for body swapping. However her Latin name of Capiocorpus would be more accurately translated as body taker. Between that and Harry's command of Latin, it's possible he just translated it wrong and no one bothered to correct him.
In Frank Herbert's Dune, the Water of Life is a deadly poison to most people, its use resulting in something horrible. Even more, it is made by drowning a baby sandworm, which then regurgitates the substance. The only way to use it is to have a Bene Gesserit drink some and convert it to a safe narcotic substance.
The Butler family are in no way servants to anyone, as lampshaded by Quentin Butler (who married into the name).
The Butlerian Jihad has nothing to do with any Muslims or any spiritual journey. The actual Buddislamics wanted nothing to do with the war. It was declared by people worshiping the Orange Catholic Bible.
Sand trout are tiny slugs that do not even remotely resemble a fish.
A no-ship is very positively a ship. Same goes for a no-chamber. The idea is that they exist in "no-space," where the Guild can't see them with their powers. So, it's circuitous, but it does make sense.
The eponymous planet of Stanislaw Lem's novel, Eden, was named from how it looked from a distance. It proved to be a distinctly Ironic Name, after the heroes make an emergency landing on it.
The Handmaid's Tale: In-universe, the Rachel and Leah Center — it's designed to train women to do what Bilhah and Zilpah did for Rachel and Leah, not to be like Rachel and Leah.
The Heroes: Whirrun of Bligh has never even set foot in Bligh and has no idea why he's called that. He's actually from a land no one has ever heard of, and Bligh is simply the farthest land anyone knows.
The Perfectly Normal Beast in The Hitchhiker's Guide to the Galaxy: it is actually fairly normal, except that it only appears on the planet Lamuella in a stampede from one invisible space warp to another. It was named to reassure residents, but Trillian at least finds the name suspicious instantly.
For the longest time, the series itself was called "a trilogy in 5 parts", with Mostly Harmless further lampshading this by calling itself "the fifth book in the increasingly inaccurately-named Hitchhiker's Trilogy." And And Another Thing... is billed as "Part Six of Three" on its cover.
In-universe example in Jurassic Park: it's noted by at least one character that the dinosaurs in the park aren't from the Jurassic. Evidently the park's creators went for "sounds good" rather than "accurate".
The opening sentence of Salman Rushdie's Luka and the Fire of Life reads: "There was once, in the city of Kahani, in the land of Alifbay, a boy named Luka who had two pets, a bear named Dog and a dog named Bear, which meant that whenever he called out, "Dog!" the bear waddled up amiably on his hind legs, and when he shouted, "Bear!" the dog bounded toward him, wagging his tail."
The Narrator of McAuslan has enormous trouble figuring out the identity of someone in his regiment who bears the nickname "Darkie". He becomes even more confused when he figures out that "Darkie" is white, light brown-haired, blue-eyed and him.
In Odd Hours, Odd mentions how the streets in Magic Beach all have non-indicative names. Jacaranda Avenue has no jacaranda trees, Sterling Heights is the town's poorest neighborhood, Ocean Avenue is the farthest street from the ocean, Memorial Park Avenue doesn't have a memorial park on it, and so on.
There is an old riddle that inquires who is largest among Mr. Mrs. Bigger and their child. Answer: The child, because he is a little Bigger.
Tock is a watchdog who could only go "tick." His brother, named Tick, could only go "tock." It's a sensitive subject in their family.
The Giant, the Midget, the Fat Man and the Thin Man are really one ordinary guy holding four jobs. He justifies this as follows:
You see, to tall men I'm a midget, and to short men I'm a giant; to the skinny ones I'm a fat man, and to the fat ones I'm a thin man. That way I can hold four jobs at once.
Arthur Phillips' 2003 novel Prague takes place entirely in Budapest (the characters think everything is happening in Prague, and talk about it but never go there).
The Princess Bride isn't technically a princess; Buttercup was the daughter of a dairy farmer, but as she was almost inhumanly beautiful, Prince Humperdinck had insisted on her being his bride. His advisors, troubled by the idea of him marrying a non-royal, quietly arranged for her to be known as the Princess of Hammersmith (a tiny portion of the realm) and shipped her off to royalty school for training. (The film version makes no attempt to hide the fact that she was born a commoner.)
Redwall has a clever one: Nobody seems to know what a "Walking Stone" is. Turns out, it's a tortoise.
The Reynard Cycle: In The Baron of Maleperduys, a mercenary company called The Seventy Seven Shields turns out to be made up of one hundred and thirteen people.
Not only is Macros the Black Sorcerer not a villain, but he wears brown robes, in contrast to most other wizards in the series. Justified as his name was part of a series of tales designed to keep people from approaching his island home base (which he could deal with but would be a hassle), and for that matter most Midkemian magicians didn't wear black so it was more unique. The Great Ones of Kelewan did however.
Nakor the Blue Rider, when first seen, is on foot and wearing an orange robe. There is a brief interval between two books where he is in possession of both a horse and a blue robe, but other than that, he spends most of his time wearing other colors, and usually travels on foot.
The Incredibly Deadly Viper in A Series of Unfortunate Events is one of the least deadly creatures in the animal kingdom (and not even an actual viper either, being described as something similar to an even more laid-back Burmese python). Uncle Monty named it that to play a joke on the Herpetological Society.
In Death of Antagonis, planet Antagonis is blown up one third into the book, and the story itself focuses on rise and fall of Taharan rather than anything connected to Antagonis.
In Purging of Kallidus, the eponymous harbor is purged off-screen by PDF Red Shirts, while the heroes go around purging power plants.
The Star Wars Expanded Universe is as big of an offender as the movies. Among those mentioned already under the movies, there's also the Sun Crusher, which doesn't crush suns, instead causing them to go supernova and rip apart in a violent explosion.
A Streetcar Named Desire has very little to do with streetcars named Desire other than the fact that one of the main characters arrives on a streetcar named Desire.
A "death spell" makes people think someone is dead.
The "maternity" spell creates one-way synchronization between the caster and the target, essentially making them a hostage to the caster's well being.
To a degree the Confessors, who brainwash people into being their slaves. They're called that because they're supposed to use the ability to make people confess to their crimes. But in the series it's mostly just used to enslave people's minds.
L. M. Montogomery's A Tangled Web featured Little Peter and Big Peter. Unfortunately, they were named when children, and Little Peter is the younger by ten years. Now that he is a foot taller, the names are stuck.
The Three Musketeers is somewhat of a misleading title, as it refers to Athos, Porthos, and Aramis, who are actually co-stars to d'Artagnan, the true protagonist. Further, the titular Musketeers are only once seen to be in possession of muskets — virtually all of the fighting is done with swords or pistols.
In the alternate timeline detailed in Harry Turtledove's Timeline-191 series, America gets involved in a conflict called The Second Mexican War in the 1880s. Despite its name, the war wasn't fought against Mexico (unlike the First Mexican War) and only part of it took place South of the Mexican border. The war was fought between the United States and the Confederate States, and the part of Mexico where the fighting took place was technically part of the Confederacy at the time.
The Unexplored Summon://Blood-Sign: The White Queen's full name is "The White Queen who Wields the Sword of Unsullied Truth". The Sword of Unsullied Truth is actually her dress, which can transform into various weapons (including, but certainly not limited to, swords).
The Wakefields of Sweet Valley, a prologue novel to the Sweet Valley High series, is about a family of women not named Wakefield who do not live in Sweet Valley.
In Warren the 13th, each of the 3 witches has a "spirit animal" that they can transform into. It turns out that Aunt Annaconda's spirit animal form is not a snake, but a snail.
One of Isaac Asimov's earliest published stories was titled The Weapon Too Dreadful To Use. As you've no doubt already guessed, the weapon is in fact used. Asimov later noted that having this disconnect pointed out to him soured him on using grandiose titles.
Lampshaded in the very first line of The Westing Game. Sunset Towers is an apartment building that faces east (sunrise), not west— and has no towers.
In Stephen Baxter's Xeelee Sequence, a government known as the "Interim Coalition Of Governance" rules humanity. It stands for an "interim" period of roughly 20,000 years.
In the Author's Note at the beginning of Zen and the Art of Motorcycle Maintenance, Pirsig tells the reader, "However, [this book] should in no way be associated with that great body of factual information relating to orthodox Zen Buddhist practice. It's not very factual on motorcycles, either."
The Australian Women's Weekly comes out once a month. Well, they could hardly call it the "Australian Women's Monthly" could they??!!
Rosemary Wells' young adult novel "Through The Hidden Door" falls afoul of this. The "Hidden Door" is only referenced midway through and is barely relevant to the plot, which is mostly about bullying and a cave.
Perry Rhodan is called "Heir of the Universe" (even more so in the comics). Whoever owns the universe probably hasn't died yet. It's possibly a metapher anyway.
In The Witchlands, the Dalmotti Empire is actually a republic-slash-oligarchy, ruled by elected Guildmasters, who in turn elect the Doge to preside over them.
In the Warrior Cats series, Cloudstar's Journey isn't actually about a journey. The emotions he experiences in it could be called one, but that's a bit of a stretch, and considering that we knew from other books that the character does eventually lead his Clan on a literal journey, fans were expecting that to be what the novella was about.