No character is actually named "Cowboy Bebop". "Cowboy" is an in-universe slang term for bounty hunters, and the ship used by the main group of hunters is named the Bebop. See also Cowboy BeBop at His Computer. It also doesn't help considering names are rarely spoken.
Many people confuse the name of the villain Mad Pierrot with the episode in which he appears ("Pierrot Le Fou"). Though since he appeared in one only episode, where his name is rarely mentioned, it's understandable. Particularly since "Pierrot le Fou" means "Mad Pierrot" in French...
Even the back cover of the DVDs makes this mistake: "A new generation of outlaws came into being. People referred to them as Cowboy Bebops."
The heroine of The Vision of Escaflowne is named Hitomi, not Escaflowne. Escaflowne is, of course, a giant mecha. Escaflowne does not have the vision, the vision is depicting Escaflowne.
The main character of Aria is Akari, and Aria is the name of the company she's working in (although it's a namesake of the president)
The teacher/main character of Sayonara, Zetsubou-Sensei prefers to be called Itoshiki Nozomu. He freaks out when his name is written horizontally, however, because it spells out "Zetsubou", which means "despair".
Magic Knight Rayearth is not the name of the Magical Girl team featured, who are just referred to as the Magic Knights (plural). It specifically refers to the lead Genki Girl and her mashin named Rayearth. The OAV attempts to change this by changing the name of the Mashin to "Lexus" and Rayearth is all the knights' fused Mashin.
"Hina" in Love Hina doesn't refer to any of the main characters, but to the name of the inn where characters live, itself named after Keitaro's grandmother.
The main character in the series Tenchi Muyo! is named Tenchi Masaki. The title of the series is a complicated Japanese pun (involving, among other things, the standard Japanese labeling for "This End Up!"), and not the name of the main character. This caused some confusion when the movie Tenchi Muyo! In Love came out, because misreading the title as the name of the main character implies that Tenchi falls in love in the movie, which he doesn't. The title is most easily translated as "No Need For Tenchi", which fits in with the Idiosyncratic Episode Naming.
Also, Ryoko has been called "Tokoton Ryoko" on at least one fan web site. Tokoton Ryoko is actually the title of a book about her, and means Thoroughly Ryoko. Her name is in fact just Ryoko, although she is sometimes (but never to her face) called Ryoko Hakubi, due to her relationship with Washu in the OVAs.
The protagonist of Trigun is known as "Vash the Stampede". No one is certain what the title refers to, the most popular idea being his three weapons: the silver revolver, the machine gun hidden within his prosthetic arm, and his Angel Arm. This confusion was lampshaded during the Adult Swim broadcast of the show. One of their bumper cards accidentally referred to Trigun, the show, as "he." This resulted in a ton of angry emails to AS about how the character's name is Vash, not Trigun. AS responded by creating a new card which intentionally confuses the two. "Can Trigun escape? Will his marksmanship be enough?"
The main character of Sumomo Mo Momo Mo is named Momoko, not Sumomo or Momomo. But most people are just lucky to say the tongue-twister title correctly, so try to cut them some slack on getting the characters right, too.
When City Hunter was adapted to Italy, Ryo, the main character, had his name changed to... City Hunter (Hunter was the first name, City the surname, apparently).
Of course by Angel Heart people who don't know Ryo very well are calling him "City Hunter" the same way people will call Hal Jordan or Allan Scott "Green Lantern".
This was also prevalent in the original City Hunter manga, where "City Hunter" (often rendered "CH" in English with Japanese furigana above it in dialogue balloons) was implied to be the name of Ryo and Kaori's organization.
A lot of people who are not anime fans think Dragon Ball is the name of Son Goku.
Even worse, Goku and his friends are sometimes referred to as "The Dragonballz".
Another common mistake is referring to the Energy Blasts that became staples of the series as Dragon Balls
When YuYu Hakusho came to Israel and was dubbed into Hebrew, Yusuke Urameshi's name was changed to...you guessed it... "Yu Yu Hakusho".
The Netflix description of the movies is worse. One of the movies refers to him as Yu Yu Hakusho, the other Yu Yu Urameshi, and the series itself correctly identifies him as Yusuke Urameshi.
Anime fans have a meme from the period where WWE Smackdown advertised the Dark Tournament video game with color commentator Taz proclaiming "Yu Yu Hakusho! I love that guy!" in each and every ad.
Tokyo Pop is guilty of this; in their translation of Tokyo Mew Mew, Mew Ichigo was initially referred to as if "Mew Mew" was her name. In fact, "Mew Mew" is a title granted to all the series' Magical Girls. When the group is given the name "Tokyo Mew Mew" in the second volume, the translators realized their mistake and started calling her Mew Ichigo. Too bad they didn't fix everything, though.
Due to the title, there's confusion over the name of the protagonist in Mahou Sensei Negima!. It's "Negi", not "Negima" (and as of this writing, the author has not given a reason why there is an extra "ma" in there). note Also, the extra "ma" is written with a hiragana character, while the protagonist's name is written with katakana characters "ne" and "gi", which further underlines the fact that this is actually a compound word. The only time it's mentioned is during a Title Drop. Negi's friends briefly call themselves the "Negima Club" until Evangeline makes them change it. See the manga's Fridge Brilliance page for a possible (spoilerific) reason for the -ma at the end.
The manga Rin isn't named after a character, but is a kanji used to refer to something that gives one shivers of awe.
Tsukimiya Ayu's name is not Kanon, nor is it the name of any other member of the Unwanted Harem. Kanon refers to Kanon D-dur, a piece of German classical music known in English as "Canon in D" or "Pachelbel's Canon".
AKIRA is not the name of the main character of the manga, he's named Kaneda. His best friend who gains superpowers and goes insane also is not Akira, he's called Tetsuo. The strange creepy child that gives Tetsuo the superpowers? No, he's Takashi. In fact, Akira doesn't show up during the entire first volume and is more like a living MacGuffin.
Nobody in Dr. Slump is named like this. It's a insulting nickname for Bungling Inventor Senbei Norimaki; the Dragon Ball Wiki compares this to nicknaming an author "Writer's Block". The pilot of the failed Harmony Gold Macekre of Dr. Slump sometime back, indeed renamed Norimaki as "Dr. Slump".
Before Yotsuba&! got its official translated name, a lot of folks thought the main character's name was Yotsubato. Despite the fact that the Japanese manga books say "Yotsuba&!" on the back cover.
Chobits is not the name of the female lead of the series (of the same name). It's Chii. "Chobits" is the class of persocom that Chii is implied to belong to. It turns out, she is one of them.
Knowing that Yu-Gi-Oh means "King of Games," it's not unreasonable to believe that it's one of the things he's known as. Since he is a Pharaoh, he likely has titles like this. In fact, the opening monologue in the Japanese version states "People refer to him as 'Yu-Gi-Oh'" (though presumably as a title rather than an actual name).
Saying he's known as Yami could be Fridge Brilliance, in that he's correct: it's the name the fans use for him. So, he's being meta.
The Italian intro actually starts with the lyrics "Yu-Gi-Oh, Yu-Gi-Oh! That`s your name!", and a german kids magazine about Anime constantly called Yami Yugi "Yu Gi Oh" in their commercials.
The heroine of Princess Mononoke is named San, not Mononoke. Mononoke is just the type of demon that the residents of Irontown believe her to be. Additionally, she's not actually a princess, either. In fact, Mononoke Hime started as a very old and completely different story concept in the 80s in which the title character was referred to as "Mononoke Hime" because she would be marrying a mononoke. The title was retained on the film that eventually became the one we have today, but since it was so radically different and centered around a different character, Miyazaki wanted to change it to "The Legend of Ashitaka". He was convinced not to over some superstition at Studio Ghibli — all of his films, in Japanese, contain the character for "no". "The Legend of Ashitaka" was "Ashitaka Sekki". The studio didn't want to ruin their good luck with his films by not maintaining the "no" tradition.
Perhaps to avoid this confusion, the English dub mentions "Mononoke" only once in dialogue. A few other instances seem to have been glossed as "wolf girl."
The back of the 2010 box refers to her as "the brave Princess Mononoke", however. Oops.
Lum and the other Onis in Urusei Yatsura come from the planet Oniboshi. The title is a complicated Japanese pun that is partly based on "urusai" and "-sei" (meaning star or planet, the same kanji used for -hoshi/-boshi). The meaning of the title was explained in the Viz manga, so it became widely known, and fans have misinterpreted that as meaning that Urusei is the actual name of the planet. Fanfic then spread it further.
Urusei Yatsura means literally "those noisy guys", but idiomatically refers to annoying next-door neighbors. Combining the idiom with "sei" makes it something like "those noisy other-planet neighbors".
You could do roughly the same gag in English with "Annoyliens".
Or as AnimEigo puts it, "Those Obnoxious Aliens", which also has the fun of sounding like a '50s sitcom.
Fullmetal is a pun in the original language. "Hagane" was translated to "Fullmetal" when it came to America, and in the original language it means both "steel" and "stubborn", referring to his limbs, his brother and his personality at the same time.note Unfortunately, something like "Steelborn", while sounding cool, wouldn't have gotten the "stubborn" part across well either, so there's not much they could've done for this one. "Fullmetal" does sound kinda hardcore, though, which you'd have to be to go through Training from Hell to learn to use human transmutation while still a kid, so it works in its own way.
The English dub of the first anime briefly made this mistake itself; in the eighth episode, Roy refers to Bradley as "the king" as if it were his title. This was fixed in later episodes.
The name of the country it takes place in is not "Shamballa", despite the name of the film for the first anime; it's "Amestris". Dietlinde Eckhart only thinks that Amestris is Shamballa because... well... no apparent reason, but considering she'd never actually been there, she had no idea what to expect. But really, a Buddhist paradise located in Asia where everyone is enlightened has nothing in common with a heavily militarized nation based off of Europe that you access by a dimensional portal.
In the Violinist of Hameln manga, the hero's name is Hamel, and he is going north to the Mazoku city Hameln (the name of which comes from the fairy tale about the Pied Piper of Hamelin). The anime never told us the name of the Mazoku capital, but kept the title Violinist of Hameln, making it seem like Hamel's name was actually Hameln.
Streamline Pictures' dub of the Fist of the North Star movie made it seem as if "Fist of the North Star" was a title that Kenshiro and his brothers were fighting for rather than the name of their martial art style Hokuto Shin Ken (The Divine Fist of the North Star), which can only have one successor per master. It should be noted that the Japanese title, Hokuto no Ken, is an Epunymous Title. The name "Ken" is a homophone for the Japanese word for "fist" or "martial art". Thus, Hokuto no Ken can refer to the martial art of Hokuto Shinken (as in the "martial art of Hokuto") or the main character himself, who is named Ken (as in "Ken of the Hokuto school"). This play on words is lost on the English title.
In the Brazilian dub of Kaleido Star, the dubbers for some reason decided to change the name of the Kaleido Stage to Kaleido Star, most likely for easier recognition. The term "Kaleido Star" is used in-show as the title to the best artist of the circus. In the Brazilian dub, this term became "Estrela do Kaleido Star" (literally, "The Star of the Kaleido Star").
Not a character, but similar, is a situation with Ranma ½ and the Kachu Tenshin Amaguriken. This is a type of Training from Hell in which the trainee attempts to pluck chestnuts from amidst open flames in order to boost their speed, and Ranma later uses this training to develop a Rapid-Fire Fisticuffs attack that becomes the keystone of his subsequent battles. He never actually names this in the manga, but the anime and video games evidently mistook the training for the technique and, thanks to Calling Your Attacks, it became an established part of Fanon.
There's also the awkward case of Pantyhose Taro. Just like more traditional names like Kentaro, Ryutaro, Sentaro, or Yotaro, his full Japanese name would be "Pantsutotaro" as one word (thanks to the perverted Happosai, who baptized him, replacing an ordinary prefix with something more to his tastes.) However, "pantsuto" literally means "pantyhose," making it awkward at best to transliterate his name into "Pantyhosetaro." Thus, for the sake of aesthetics, his name is typically displayed in English (both in official translations as well as Japanese materials) as "Pantyhose Taro." Fans, however, took to referring him by his "first name" Pantyhose or his "last name" Taro, which would be akin to calling some one "first name Ro, last name Bert."
This happens often with Hellsing. The title refers to the vampire hunting organization which is named "Hellsing" after the family who founded and runs it. The current head of the Organization is named "Integra Hellsing" and she employs a vampire who hunts other vampires named "Alucard". He's the main character who is featured most on book and DVD covers. Almost always, when someone with no knowledge of the series takes a look at it or comments on it, they tend to call Alucard "Hellsing".
"Blackbird" (or sometimes "The Blackbird") is the extensively-tuned Porche driven by Tatsuya Shima, not the doctor himself. However, his identity is so tied to that vehicle and street racing (Akio and Reina at least occasionally hang loose and have some fun) that a lot of readers and Maximum Tune players now call both entities Blackbird. This was adopted in the anime adaptation.
In a rather odd variant, Axis Powers Hetalia's Italy refers to himself as Hetalia in the credit song. This is likely because since "Hetalia" is a portmanteau of "hetare" (lovable idiot) and "Italia", he meant something along the lines of "I'm Idiot Italy!" However, his name is still Italy and not Hetalia.
The English name of the series is an odd example. It's actually an Altum Videtur subtitle/translation of the Japanese title, "Mahou Shoujo Madoka Magica" ("Magical Girl Madoka Magica"). "Puella Magi" appears exactly zero times in both the original Japanese track and English dub; the heroines are always referred to as Magical Girls. Nonetheless, this term is often used in the fandom as an alternate name for the heroines, since it's a convenient way to distinguish them from Magical Girls in general. However, in the sequel, the protagonists do refer to themselves as the "Puella Magi Holy Quintet", but only once, and it's during a very strange sequence which can be construed as mocking the fandom.
Kanamemo lampshades its title on an omake in the manga, also referring to infamous examples such as the Die Hard and Avatar examples:
Kana: Supposedly it's a pun on the word memorandum, since "Kanadiary" wouldn't catch on, wouldn't you agree, Yume?
Yume: I'm just worried that it's gonna have the John McClane or Na'vi effect.
Saki: Ugh, I hate that.
Pani Poni Dash! is not the name of the school that Becky teaches at. The school is called Momotsuki Academy. The term "paniponi" is used in-show, but it's unclear exactly what it means.
Koharu Biyori is not anyone's name in the series. It translates into "Indian Summer" which it was retitled for its North American release.
InuYasha: Inuyasha and Sesshoumaru's father is known as "Inu no Taishou". A lot of fans think this is his name but it's simply a title roughly equivalent to "the Dog General". His name is never revealed.
The usual Frankenstein flub is parodied in Baccano!, where Isaac corrects Miria for making the error: Frankenstein was the scientist — The monster's name was Mary Wollstonecraft Godwin Shelly.
A Norwegian boy wanted to change his name to Sonic X after the character from the anime of the same name. The problem... Sonic doesn't really have a surname, and it certainly isn't X.
This was a common issue when the anime was popular. It caused a Newbie Boom of new Sonic fans, however if you read forum posts or fanfics you'll see that many children didn't realize that Sonic's name wasn't "Sonic X".
Astro Boy: Has anyone ever actually referred to him as "Astro BOY" in-universe? Astro's name is simply "Astro".
In the aborted Robotech II: The Sentinels, the Sentinels doesn't really refer to the members of the Robotech Expeditionary Force. It refers to a multiracial group of aliens form Invid occupied planets. The REF assists them in liberating their worlds. Some of the REF members do end up fighting alongside the Sentinels but they were not charter members and were still mostly associates.
That guy known for defeating his enemies with one punch? He's never called the One-Punch Man. He's only ever addressed by his real name, Saitama, or his super hero name, Caped Baldy (he didn't pick it).
The main character from Steins;Gate isn't named Stein. His real name is Okabe Rintarou, and he refers to himself as Hououin Kyouma. The name comes from his Catch Phrase, "This is the choice of Stein's Gate!", which he uses to refer to any interesting developments.
Mirai Nikki doesn't refer to any character in the series. It's Japanese for "Future Diary", which refers to the diaries that can help learn about future events, that are given to each contestant.
The protagonist in Hana no Ko Lunlun is called Lunlun, not Hana. This is a understandable mistake to make if you have not watched the anime since Hana is a common Japanese name for girls while Lunlun just sounds nonsensical.
The Suzy's Zoo: Daisuki! Witzy anime is based on the Little Suzy's Zoo sister franchise, not the main Suzy's Zoo one (the latter has Suzy Ducken, Jake Quackers and Corky Turtle and targets an older audience).
Sgt. Frog: Dub example—While making Ikinari dumplings at lightning speed on an assembly line, Angol Mois mentions feeling "just like I Love Lucy in that episode of I Love Lucy".
A real-world example is Keroro's name. Initially, there was confusion that caused some English readers to call him Sergeant Frog, since even though his name wasn't changed for the English release, that was the name the series got. Most people know better now, though.
In the English dub of Space Battleship Yamato (known as Star Blazers), the crew is not called the Star Blazers in any dialogue. They are always called the Star Force. In the recap narration for each episode, the narrator, however, does say "a team of Star Blazers called the Star Force...", which does sound somewhat odd.
There is no character in Charlotte named "Charlotte". The title refers to a comet, which emits particles into the atmosphere when it transits Earth. Children who breathe in these particles develop superpowers.
Action Heroine Cheer Fruits: The girls' fictional superhero team is called "Hina-Nectars", while "Cheer Fruits" is the name of their production team. This phenomenon is actually discussed in Episode 4, where Misaki mentions that the popular heroine Kamidaio belongs to a production team called Gingers, but most people just use the Kamidaio name because it's far more prominent.
None of the girls in Azumanga Daioh are named "Azumanga". It's just a manga written by Kiyohiko Azuma and published in Dengeki Daioh magazine.
The girls of K-On! are in a band. Their band's name is "Afterschool Teatime", not "K-On".