In general, any game with a less obvious title that doesn't include the main character's name runs the risk of this. Of course, there are plenty of games that do have the main character's name in the title, so the confusion is understandable.
From the The Legend of Zelda series, we have...Zelda. A number of people seem to be under the impression that Link, the protagonist, is named Zelda himself (which in turn causes some people to believe Link is a girl). Zelda is, in fact, the princess. This is one of the offenses that causes one to hit the Fandom Berserk Button.
The fact that the games allow you to name Link anything you want means that, if you like, you CAN make "Zelda" the main character. In fact Zelda is the second most common thing for players to name Link (after, well, Link). This is partly Nintendo's fault, as they gave players a reason to do it — one of the biggest open secrets in the NES era was that using ZELDA as your name in the original The Legend of Zelda unlocks the second quest early. And in most games since, naming him Zelda unlocks some other Easter Egg.
Tomb Raider is not Lara Croft's name; it's her vocation. The first second game was called Tomb Raider starring Lara Croft, but this is still occasionally an issue. Recent games (and the movie) have altered the series name to Lara Croft: Tomb Raider.
The XBLA/PSN game eschews "Tomb Raider" altogether, and is called Lara Croft and the Guardian of Light.
Metroid is named after the parasitic aliens that appear throughout the series. The main character is Samus Aran, the person sent to kill them.
To make matters worse, several games in the series have very little to do with the Metroid species. Metroid Fusion had almost no Metroids in it, and the story revolved around its natural enemy, the X Parasite. In that case, the heroine was part Metroid due to being given Metroid DNA in the game's intro to save her from an X Parasite infection, so at least it came the closest to escaping the trope. Metroid Prime: Hunters featured no Metroids at all, except in the demo version bundled with the launch editions of the DS.
This was apparently retconned to change "Metroid" into a Chozo word meaning "great warrior", and used to describe Samus as well as the species. And also making Samus part-Metroid early in Fusion, as mentioned above.
Nonindicative Name. Nintendo of America was clearly struggling to come up with a title that would give some idea of what the game was about without being too unwieldy. (For the record, the original Japanese title is "Hikari Shinwa: Palutena no Kagami", which references the goddess Pit is trying to rescue, not the hero himself.)
Discussed by Sakurai saying that the hero in The Legend of Zelda is Link, not Zelda; Metroid is the name of the alien creatures fought by Samus; and that the angel's name in Palutena no Kagami is Pit.
The latter show also referred to "Metroid" as a universe and later as a planet. As they apparently didn't know anything about the Metroid games except that Mother Brain was in it, this should come as no surprise.
Some people call Sonic the HedgehogSonic X, after the title of the latest cartoon/anime based on the games. 4Kids themselves refer to Sonic the Hedgehog as "Sonic X" on their website. Even more baffling, since the dub itself IDs the character correctly.
Even better — pretty much every country that bought the 4Kids version were apparently told to use the "Sonic X" name for the character (in promotional materials, ads, etc.. Not in the series itself). And pronouncing "X" in English, no less.
Halo refers to the massive ringworld superweapons, not the main character who's generally referred to as Master Chief.
Star Fox refers to the mercenary team from the game rather than its leader, Fox McCloud.
Parodied in one ending in Command, where Falco's team is called Star Falco.
This confusion is understandable since throughout Star Fox 64, all the enemy characters keep addressing the player as "Star Fox". They mean the entire team, but it's easy enough to think that they're just talking about Fox McCloud. There's also one instance where Fox is entirely alone, yet Andross still calls him "Star Fox". Fox himself is only called "Fox" by his allies.
Also applies to Star Wolf, a rival team to Star Fox. The leader is named Wolf O'Donnell, not "Star Wolf".
Tales of Symphonia. 'Symphonia' is not the name of the combined worlds, nor is it the name of the tree. The tree's name is Yggdrasill. Although admittedly you don't learn the true names for the world or the tree until you play Tales of Phantasia.
In Tatsunoko vs. Capcom people call Yatterman-1 simply Yatterman. Yatterman is actually the name of the team, and Yatterman-1 and Yatterman-2 are the aliases. Similarly with Karas; that's closer to his title or even his race than to his name (Karas are humans empowered by making a contract with the "Will of the City", giving them jurisdiction over a particular city on Earth; the Karas in TvC—the main character of the OVA — is actually named Otoha).
The protagonist of Grim Fandango is named Manny Calavera, not "Grim Fandango". The title of the game is a metaphor for death that is used in one character's poetry.
A common mistake is to think that there is a character named Banjo-Kazooie in the Banjo-Kazooie games, but it is in fact a combination of names of the main characters, a bear named Banjo and his friend, a bird named Kazooie.
Also Banjo-Tooie. Many thought there was a character added named Tooie, which there wasn't. This was lampshaded in the ending of the first game: Kazooie thought that by the title she was going to be replaced by someone named Tooie.note In case you haven't got it yet, it's the second game: phonetically, Banjo-2-ie.Banjo-Tooie players are justified, however, in using "Banjo-Kazooie" as shorthand for Banjo and Kazooie together, since Split Up allows playing as Banjo or Kazooie separately, with different moves.
Similarly, in Twisted Metal, there is an ice-cream truck with a giant clown head atop it. This is Sweet Tooth. The driver of Sweet Tooth is a flaming-headed Monster Clown. His name is Needles Kane. The 989 games got this mixed up, calling both the car and its driver Sweet Tooth; once Incog, Inc. (formed by former SingleTrac employees) got the rights back, they restored Needles Kane's proper name back to him.
Not helped by the fact that TV ads for Twisted Metal III featured convicts spreading the news that Sweet Tooth got out of prison recently.
Twisted Metal: Black also has Sweet Tooth as the name for both the clown and the driver, but it doesn't appear to take place in the same continuity as the main series.
Reading the character bios (in the form of patient files for the asylum), "Sweet Tooth" was actually the alias of Needles Cane, while it listed his vehicle as the "Tasty Treats Ice Cream Truck."
Sweet Tooth is probably the most obvious example, being the series mascot, but he's far from the only — pretty much any "character" you can name off the top of your head, from Roadkill to Grasshopper to Mr. Slam, is actually the name of the vehicle, not the driver — those ones are driven by either Captain Spears, Marcus Kane, or John Doe; Krista Sparks; and Simon Whittlebone, respectively. The two major exceptions are Mr. Grimm and Axel — these bear the same name for both vehicle and driver, as Mr. Grimm's "driver" is just an extension of itself, and Axel is physically fused with his vehicle. The fact that early games had the driver names as literally All There in the Manual and even later games more conspicuously feature vehicle names than driver names probably contributes.
Some versions, such as the 2012 game, seem to have Sweet Tooth as his clown/serial killer name.
The male main character of the Tenchu series is not Tenchu. Actually he is called Rikimaru - Tenchu just means "divine punishment" (the point of the game).
Ryu Hayabusa is not "Ninja Gaiden" - gaiden means "side story", or "anecdote".
The instruction manual for the Sega Saturn port of The King of Fighters 95 refers to principal villain Rugal Bernstein as "Omega Rugal", even when describing him during the time frame of 94, when he wasn't Omega-fied. Consequently, there are fans who refer to even Rugal's normal slightly less SNK Boss style Rugal as "Omega Rugal", despite having absolutely no qualities of his 95 or 98 Boss version.
There's also some fans who think the O. stands for Orochi.
That one is semi-understandable since the power Rugal harnesses (and what consequently destroys him in the end) is called The Orochi Power. Of course, all THIS is moot considering that in '95 and '98 Ultimate Match, he has a honking great OMEGA in his lifebar.
None of the protagonists of the Shinobi series are named Shinobi.
When Pokémon was at the height of its popularity, there were a surprising amount of people who thought the series name referred to Pikachu and Pikachu alone.
The main character in Strider is named Hiryu, not "Strider". The Japanese version avoids this problem completely by being titled Strider Hiryu and Hiryu is even referred by that title in-game (which was carried over for his later fighting game appearances). There are other Striders in the series (Cain and Sheena in the NES game, as well as Hien in Strider 2), but they're bit players compared to Hiryu.
The Bishamon featured in Vampire Savior (aka Darkstalkers 3) is not actually the Bishamon from the previous game, who managed to free himself from the curse armor of Hanya, but the armor itself, having acquired a conscience of its own. The real Bishamon appears in the ending to ward off the evil spirit that has possessed Hanya.
Adding to the confusion is that a) the possessed Hanya and Kien (the sword) still call themselves Bishamon in VS, because they like the name, and b) the real Bishamon is playable in the console versions, as Oboro Bishamon. In this case, Bishamon is in full control of the armor.
The Loco Roco are a species, and each of the different colors has their own name.
Yume Nikki means "Dream Diary", referring to the main character's diary that she writes in when the game is saved. Her name is Madotsuki, not Yume Nikki.
Fallout: The little 50's mascot is named Vault Boy, not PIP Boy, your wrist computer. Doesn't help that Tactics got it wrong.
Nor is he called Fallout Boy. That's someone else entirely.
Lampshaded in Marvel vs. Capcom 3 by Zero himself during his ending: "I'm Zero, not Mega Man Zero."
Mega Man ZX retroactively makes the title "Mega Man Zero" make sense. In the ZX series, anyone who can use a Biometal is called a Mega Man (male or female). Zero didn't use a Biometal, but Model Z is based on his data, so the term extends naturally to him.
A similar problem occurs with Mega Man X, the protagonist of which is simply named X, not Mega Man X. (Confusing the issue is the fact that in the North American release of Mega Man X2, X is referred to as "Mega Man X" a few times, though this is not the case in the Japanese version, where he is still X, just like he is in every other game throughout the series.)
When Metal Gear Solid was first released, some players thought that the title refer to the newest model of the titular mecha (which is actually called Metal Gear Rex).
The tagline for Sly Cooper And The Thievius Raccoonus was "He's one thievious, devious racoonus." Sly Cooper is not the Thievious Racoonus, that's the name of his family's book that he's trying to retrieve.
The wolf's name is Amaterasu, not Ōkami. Okami is simply a title, which means "wolf".
Okami is a Japanese wordplay, as it also means "Great god".
To be fair, her Boss Subtitles give her the name "Okami Amaterasu". This is a rather dubious example...
Inverted in case of Rainbow Six. Rainbow Six is the codename of the leader, the team is simply called Rainbow.
A lot of people in Poland refer to the red-suited protagonist of Nintendo's platformers as one "Mario Bros".
Spanish language countries aren't safe either.
Mario isn't named "Super Mario". "Super Mario" is just the name for the form he has after he's eaten a Super Mushroom, not the character's actual name.
It doesn't help that Super Mario RPG called him Super Mario in the title demo.
However calling the hero "Super Mario" is commonly used and justified in countries that have "Mario" as a common people's name.
The bald super-assassin is called Agent 47. Hitman is his profession. In Absolution however he is occasionally referred to as "The Hitman" by several people as a nickname of sorts.
The name of the family in Dragon Slayer IV: Drasle Family (Legacy Of The Wizard) is Worzen; "Drasle" is really a portmanteau of the series' title. The manual for the NES version didn't help by keeping references to "the Draslefamily."
The manual for The Adventures Of Rad Gravity says "An item you picked up on Sauria will help you defeat the deadly Trogs". Do they mean the rock-throwing reptilian creatures, or the twin robots that are the boss of the level(which require the Saurian Crystals to defeat)?
The hero of Arkista's Ring is not named Arkista, but Christine.
In the Valis series, Valis is the name of the heroine's sword. The heroine's name is Yuko, who is also known as the "Warrior of Valis" (until the Changing of the Guard, that is).
The the tall, faceless entity that's stalking you in Slender is called "The Slender Man". Despite this, a lot of people think his name is "Slender".
The protagonist of Mr. Driller is named Susumu Hori, not "Mr. Driller", which is the name of the title awarded for a No Damage Run. Even the localizations get this mixed up on occasion, and are very inconsistent about it.
In the obscure Nintendo game WURM: Journey to the Center of the Earth, the WURM of the title is a nickname for the Drill Tank your characters get around in. That name's never used outside of the title and the manual, despite the surprising amount of dialogue and story scenes for a game of its system and time. In-game it's always called the VZR.
Skullgirls is not the name of an organization that the playable characters are in. Rather, the Skullgirl is an Eldritch Abomination that serves as the main antagonist. Part of the confusion is probably because the game's original roster is entirely female.
In a rare reversal of this trope, Alice in No More Heroes 2: Desperate Struggle actually refers to Travis Touchdown as "The No More Hero" because he was able to walk away from the life of an assassin after reaching the top ranking in the first game.
In a rare video game company example, LJN has this happen. In their Enteractive Video Games, some people have mistook Enteractive (not to be confused with the company) for a separate gaming company. Enteractive was a brand label LJN used on some of their games during 1987-1990.
It is all but forgotten that the Galaxians in the 1979 game Galaxian refer to whatever space organization the player's ship (called a Galaxip in the game) works for. It wasn't intended to be the name for the race of enemy aliens. The attract screen includes the game plot summary: We are the Galaxians/Mission: Destroy all aliens.'. The name of the invading aliens' race is not stated. However, Bally seemed to forget this and referred to one of the stages in Gorf as the Galaxians (note the plural) stage. The yellow flagship has made cameo appearances in many Bally/Midway games including PacMan. It is often referred to as the Galaxian flagship but there's often confusion as to whether they mean the flagship from Galaxian or the flagship of the Galaxians. The former is technically more correct.