Halfway through the Sister Fidelma series, Sister Fidelma renounces the religious life and starts referring to herself as just plain Fidelma.
In The Demon Headmaster novels, the title Diabolical Mastermind is only a school headmaster in the first book, though he's referred to as the Headmaster throughout because that's the context the heroes first encountered him in.
After book one, The Boxcar Children spend more time solving mysteries than encountering boxcars. They got the name because they lived in a boxcar for a while, but it sticks after they don't live there any more. They do keep the boxcar as their hangout spot on the property where they live but it's still a stretch.
Several English translations of The Phantom of the Opera translate the French "fantôme" as "ghost" within the text but, understandably, don't change the widely-known title; thus, the eponymous character is never actually called "phantom of the Opera" but "the Opera ghost."
The Ranger's Apprentice series, after Will graduated from being an apprentice to being a full ranger.
In-universe in Fall of Damnos. Captain Falka's command is called the One Hundred, but it's unlikely there were ever one hundred of them, and there certainly aren't that many now. They keep the name, though, because it sounds nice.
Used in-universe in The First Law, particularly in The Heroes. Units of fighters in The North are referred to as "dozens," even though almost none of them contain a full twelve men anymore. The primary dozen followed in the novel is explicitly stated to have never had a full twelve in its twentysomething years of existence.
The Foundation Trilogy has an in-universe example. At first, "The Encyclopedia Foundation" was a N.G.O. focusing on the publishing of a compendium of all human knowledge. While they did eventually do that (sort of), the Foundation focused more on the Seldon's plan, and became an empire. A second example is the position of Mayor of Terminus, which was still used for the top position in the Foundation government even after the Foundation had grown from the single city on Terminus to roughly half the Galaxy.
Inverted with Francine Riversí The Mark of the Lion trilogy, in which actual marking by lions doesn't feature until the very end of the first book, and doesn't feature at all in the third. (Though it could easily be inferred to be an important metaphor, what with Jesus being referred to as the Lion of Judah.)
I, Robot. Its title was borrowed from an earlier story by Earl and Otto Binder. Not a single story in Asimov's book is told from the perspective of a robot. Even better, Asimov is reported to have detested the title, which was forced on him by the editors. Also, an in-universe example shows up: USR, the robot manufacturing corporation at the center of the plot, continues to call itself "United States Robotics" long after the United States has ceased to exist as a country.
Half the titles forget that Shannara is not the world, but a historical figure. This reaches its nadir with The First King of Shannara, which is about that historical figure and might better be titled King Shannara. Since the books follow the exploits of the descendants of Jerle Shannara, it could be argued that he is the first king of the Shannara line. But all the titles would make more sense if "Shannara" were replaced by "the Shannara bloodline" or "the Shannaras" or even "the Ohmsfords" since Jerle's family spends most of history with a new surname.
Played straight in the most recent series, titled "Genesis of Shannara" and "Legends of Shannara". They take part long before the historical figure even existed and the only "genesis" in the first series is a new world.
Similar to the Hitchhiker's Trilogy, Robert Rankin's Brentford Trilogy currently has nine books.
In the Rainbow Magic series, only the first seven books dealt with the rainbow.
Reversed in Dinoverse. Dinosaurs are involved from the start, but it's time travel, not The 'Verse-y at all. It's only in the last two books that an alternate universe called Dinoverse comes up.
In Vampire Academy, the second, fourth, and sixth books take place primarily outside of the eponymous St. Vladimir's Academy.
The fourteenth book of The Morganville Vampires spends only the first and last chapter in the city of Morganville, mostly spending its plot near MIT.
In The Bible: There are two Books of Samuel. Samuel dies halfway through the first book; after that, we follow Saul, whom Samuel had anointed as king by God's command. After Saul falls from grace before God and becomes a villain, David is the protagonist. This is more due to the books being written by the scribes of David—who became king after a long conflict with Saul—so the naming of the second book is a slight to Saul.
A few novels into the Star Trek: Enterprise Relaunch series, the titular starship is irreparably damaged. The series continues with Captain Archer promoted to admiral and the rest of the crew split up across two new ships captained by T'Pol and Reed.
When the first book of the Rivers of London series was translated into French, the publishers wanted a less London-centric series title, and settled on Le Dernier Apprenti Sorcier, "The Last Sorcerer's Apprentice". A reasonable attempt, given they only had the contents of the first book to go on, but one that has become less accurate with every subsequent book. By now it is very clear that Thomas Nightingale is far from the last active sorcerer, and nor is Peter Grant the last apprentice he takes on in the course of the series.
John Dies at the End began as a web serial, and the title might have been true at some point, but in the completed novel John "dies" midway through the story, gets better, and is not even teased to die at the end.