Possibly Ur-Example: Frankenstein is not the name of the monster, but the last name of his creator. The monster does lay claim to it towards the end of the book though, considering himself the Doctor's son more or less.
Even the directors of the movies seem to have made this mistake, as the movie Bride of Frankenstein is actually about the bride of the monster.
Tired of nitpicking, xkcd "resolved" the issue by making its own version of Frankenstein where it is the monster's name, so that people can say that is their canonical version.
The Inferno is the first (and most famous) part of Dante Alighieri's epic poem The Divine Comedy. This part of the poem and in particular its images of Hell is often referred to as "Dante's Inferno", but people often take this to mean that the whole poem is titled Dante's Inferno, assuming Dante to be a character or other part of the narrative, rather than the writer.
Well, Dante is the main character of Inferno (as well as Purgatorio and Paradiso). It's just a different Dante. Well sort of. It's up to interpretation. The point is that the title is not Dante's Inferno
Subverted in Maximum Ride - despite sounding like something else, Maximum Ride is in fact the narrator and main protagonist's name.
The Lord of the Rings is Sauron, the Big Bad, not any of the heroes in the series. This misunderstanding is already cleared up in the book: Pippin at one point calls Frodo the "Lord of the Ring", only to be hastily corrected by Gandalf — the One Ring serves only one master and bends all others to his will. Frodo later titles the Red Book of Westmarch as The Downfall of the Lord of the Rings and the Return of the King. The popular live-action film version also pointed this out ("There is only one Lord of the Rings, and he does not share power"), so there's probably less confusion on this one nowadays.
Referenced in the book Are You A Geek?, where one of the things that gets you points is "You get annoyed when people assume that the name of the film is also the name of the main character, shouting things like 'Come on, Die Hard!' and 'Get 'em, Total Recall!'"
Moby Dick is the whale; Moby-Dick (with a hyphen) is the book.
Many people who have not read Rebecca, or who do not remember it very well, refer to the narrator by that name. It is actually the name of her husband's first wife, who is dead before the story begins. The narrator's name never comes up.
Parodied in a Mitchell and Webb sketch. Hitchcock's Film of the Book is being made, but Executive Meddling demands that if it's named Rebecca, it has to be about Rebecca. They don't change the names, though, they just replace all instances of "first wife" with "second wife" and vice versa.
A variation of this would be the fact To Kill a Mockingbird is not an instruction manual for mockingbird hunters. There weren't even any mockingbirds. It's a reference to a metaphor used throughout the story. There was even a Title Drop in which mockingbirds were referenced directly, and they're a symbol for one of the growing-up lessons Scout learns.
Atticus: Shoot all the jays you want, but remember it's a sin to kill a mockingbird. ... They don't do one thing but make music for us to enjoy.
At the end, when Scout agrees not to reveal Boo Radley's heroism:
Scout: Well, it'd be sort of like shooting a mockingbird, wouldn't it?
This is referenced in Failure to Launch, when Zooey Deschanel's character is annoyed by a mockingbird outside her window. She goes to a gun shop and wants to buy one to kill a mockingbird. The clerk tells her she can't do it, and references the book. Having never heard about it, she assumes that it's an instruction manual.
The main character in Johnny Got His Gun, a fairly horrific story about a World War I soldier waking up in a hospital, is often mistakenly referred to as "Johnny;" his actual name is Joe. The title's a Literary Allusion Title to the patriotic pro-war song "Over There" (which begins with the words Johnny, get your gun).
The video for the Metallica song "One" was inspired by the film version of this novel. In an interview following the video, Lars Ulrich informs the audience that he had been deeply moved by the story of poor Johnny.
Spoofed in 1066AndAllThat, which makes Henry IV Parts I and II separate characters. Recently referenced by Richard Dawkins in The God Delusion: "'Thy wish was father, Harry, to that thought', as Henry IV Part II said to his son."
The Three Musketeers. The world may never know that there were, in fact, four of them. Though many adaptations have D'Artagnan not become a musketeer himself until the end, in the original book he becomes a Musketeer about halfway through. Actually, he's made a musketeer twice. It's seems that due to the vagaries of serialized fiction, Dumas forgot he ended a chapter with D'Artagnan being made one. Several chapters later, he's made one permanently.
Slumdog Millionaire cleverly exploits this misconception. The climactic question is "The Three Musketeers are Athos, Porthos, and who else?" Since "everyone knows" that D'Artagnan is one of the Three Musketeers, a lot of viewers think that "D'Artagnan" is the right answer and "Aramis" is the wrong answer.
Inverted in case of Rainbow Six. Rainbow Six is the codename of the leader, the team is simply called Rainbow.
The monster in Lewis Carroll's poem "Jabberwocky" is only called the Jabberwock; the title is just one more piece of nonsense verse.
He may have intended "Jabberwocky" to mean "the story of the Jabberwock", in the same way that The Odyssey is the story of Odysseus.
This is forgotten in some translations, where the name of the poem is identical to the name of the creature (e.g. in Dina Orlovskaya's Russian translation, both the creature and the poem are called "Barmaglot"; however, in Vladimir Orel's translation, the poem is called "Umzara-Zum", while the creature is just "Umzar").
Many of the books in The Wheel of Time have titles with very little if anything to do with what actually goes on in the series. A few come from prophecies and sayings in universe (only in the openings to the books where the author always sticks one of these). The biggest offender is definitely Book 6, Lord of Chaos, a phrase that the reader never actually finds out the meaning of. It's probably one of many titles either of the hero or the Big Bad, but it's never made explicit.
James Joyce's Ulysses does not literally star any character with the same name.
Harry Potter: It is "The Marauder's Map"; not "The Marauders' Map". The four people who designed it shouldn't be referred to as "the Marauders"; that name is for anyone in possession of and using the map.
It doesn't help that even some of the characters sometimes refer to the makers of the map as "the Marauders".
Possibly because they were in possession of and using the map.
L. Neil Smith's book The Forge of the Elders has an in-universe example: the giant nautiloids that sponsored the expedition (back) to Earth all have four-syllable names. The first two syllables of the expedition leader's name are pronounced "miss" and "terr", so the Americans that meet him and his agents assume that half of his name is a title ("Mister").
In "A Visit From Saint Nicholas" (aka "Twas the Night Before Christmas"), the reindeer are listed as Dasher, Dancer, Prancer, Vixen, Comet, Cupid, Donder and Blitzen. No Donner. Although 'Donner und Blitzen' would be German for 'Thunder and Lightning', which might be a more logical name pairing.
Beowulf, a murderous monster that terrorizes the land? No, the monster is called "Grendel". Beowulf is the hero who destroys Grendel.
The four protagonists of the Book of Daniel are Daniel, Hananiah, Mishael, and Azariah, who are then given the Babylonian names Belteshazzar, Shadrach, Meshach, and Abednego, respectively. However, only Daniel gets referred to popularly by his Hebrew name, while the other three are more commonly referred to by their Babylonian names, even though these names represent their captivity and forced assimilation.
Contrary to popular belief, no character in the book Alice's Adventures in Wonderland is ever referred to as "the Mad Hatter". He is simply called "the Hatter".
Rose Madder by Stephen King. The title does not refer to Rose Daniels, the protagonist; rather, it refers to the nickname Rose gives to the woman she finds inside the painting (whose real name is Dorcas).
Charlotte's Web: The titular Charolette is the Spider. The pig's name is Wilbur, and it's a he, not a she. This mistake is usually made by people who've never read the book or watched the film or Animated Adaptation, but has at least seen the book cover or heard of the book from somewhere.
The protagonists of The Berenstain Bears series are named "Bear". "Berenstain" is the surname of the authors. And, despite the common mispronunciation, it's not "Bernstein", either. Or "Berenstein," for that matter.
The main character of Flowers for Algernon is not named Algernon. His name is Charlie. Algernon is the name of the lab mouse that was given the experimental surgery that Charlie later received.
Peter Rabbit is commonly referred as "Peter Cottontail" by Americans, which isn't helped by the fact that there is a Rankin-Bass Easter special called Here Comes Peter Cottontail which also stars a male rabbit character and isn't that well-known to the public. This can cause a lot of people in the US to think that the song "Here Comes Peter Cottontail" is about Peter Rabbit when its actually about the Easter Bunny from that special. This can also be a pretty embarrassing mistake when some Americans would sometimes forget that Peter actually has a sister named Cottontail.