Fanfiction gets this a lot, as many works are named after an element of the premise that isn't necessarily required for there to be a story set in that universe, or in a different universe with similar characters.
Digimonfanfiction tends to have this problem (i.e lots of the human characters, no Digimon and if you get the Digimon, there's a decent chance there won't be any villains to battle). This is because Digimon has a LOT of fanfiction, and fanfiction is primarily a medium for the writers' romantic fantasies. Those selfsame fans complained when Frontier didn't have any Digimon partners and instead focused on the human team dynamics.
A lot of Pokémon fanfics either don't include Pokemon or barely mention them.
A lot of Harry Potter fanfiction features no appearance by the title character at all. In fact, there is a whole genre of fics dedicated to the era when Harry's parents attended Hogwarts. There's also plenty of fics about the early days of Hogwarts, taking place long before any of the characters from the books (except a few of the ghosts) were even born.
Likewise, a large percentage of Fullmetal Alchemist fanfiction does not actually include Edward Elric, the title Fullmetal Alchemist.
And by definition, any fanfiction taking place after the manga's ending doesn't include the Fullmetal Alchemist, because Ed is no longer an alchemist.
For that matter, the same logic also applies to the 2003 anime'smovieConqueror of Shamballa.
The Land Before Time features many fanfics involving time travel to the future... so... not set in the land before time then...
Most popular Rave Master fanfiction contains no reference to the rave stones at all. The biggest ones, in fact, are the ones where the characters are set in a normal universe with no magic or swordfighting of any sort.
Calvin and Hobbes: The Series has "The Transmitter Conspiracy", which reveals the so-called "conspiracy" behind the transmitter, then proceeds to go into a plot that, while still based around the transmitter, doesn't really have to do with the conspiracy.
While competition fics are common, there's a large amount of Total Drama fanfiction that deals with the characters in situations that aren't a part of competing. The most notable of these would be High School AUs, as well as any story that's set in Playa des Losers or that's focus is on a character's Backstory rather than their time in the game.
Any Teen Titans fanfic that isn't about the Titans, or ages them up so that they aren't teenagers anymore.
If a Vampire Academy fanfic is set in an All-Human AU, it becomes this by default.
Yu-Gi-Oh!'s title can refer to three things: Yugi (the protagonist), his alter-ego Atem, often named the King of Games, or just the concept of a character who could be considered a King of games. Plenty of fanfics feature no Yugi, no Atem, and no games of any kind.