Archvillain: Maira protests several times that she is not Mighty Mike's girlfriend, despite him rescuing her on a regular basis and flying her to school every morning.
Played with and lampshaded in Ryk E. Spoor and Eric Flint's novel, Boundary. A.J. and Jackie are two scientists who work together and are friends; they also bicker a lot. As such, Jackie always gets ribbed by the other people in their team about her "boyfriend" A.J. She vehemently denies these accusations to the knowing reaction of the others. Of course, when A.J. ends up with his real love interest—another scientist named Helen, which was teased earlier in the novel—Jackie smugly declares to everyone within hearing distance, "I told you he wasn't my boyfriend."
In A Brother's Price, in a rather serious situation, Cira insists that Jerin is not her boyfriend, and she is not interested in him at all. This is important, because the villains want to make a show of raping Jerin, with her Forced to Watch. She takes the fun out of it by claiming she's lesbian. She's actually rather attracted to Jerin, who, unbeknownst to him, is engaged to marry her.
In the Clémentine books, Clementine insistently states in her narration that even though he's trying, Margaret's big brother Mitchell is N-O-T not her boyfriend; though she also admits that if she ever had one, it would be him.
In book two of Codex Alera features a simultaneous "S/he is not my mate!" from Tavi and Kitai.
Averted in the Darkest Powers series. Multiple times, people talking to Derek will refer to Chloe as "your girlfriend", and while talking to Chloe will refer to Derek as "your boyfriend". They never deny it. For one thing, it's not worth it; the people taunting them about it are either bad guys looking to kill and rape them, or Jerk Asshumans mocking what they think is a schizophrenic girl. For another, Chloe quickly learns that denying a relationship between them only serves to convince people she's hiding something.
In the Deptford Mice trilogy book The Final Reckoning, the rat Barker (so called because he's "barking mad") asks Piccadilly if Audrey is his girlfriend. They are mortified, as each is in love with the other but will not admit it. Piccadilly informs Barker that he is "mistaken" and apologises to Audrey. As Barker later turns out to be the rat god Bauchan in disguise, it becomes clear that his question was not so innocent as he knew full well what their situation was.
In Dora Wilk Series, Joshua keeps telling Miron that Cute and Psycho Laoise is not his girlfriend, despite Miron's mocking (if good-natured) claims to the contrary. Seeing how Joshua is the resident Nice Guy, it's hard to say what his feelings for Laoise really are.
Pops up several times between Harry and different characters. (Harry isn't good with relationships.) His mysterious ex Elaine and police officer friend Murphy have each mistaken the other for his current girlfriend. Also, people mistook Harry for being in a relationship with Susan Rodriguez before he actually would go so far as to call it that, since he's the chivalrous type.
Later in the series, used between Harry and Thomas Raith. Thomas is intentionally acting flamboyantly gay. Harry is very open with and trusting of Thomas even though Thomas is a vampire, but he can't tell anyone the real reason: they're half-brothers. Not knowing the real reason, most people jump to the conclusion that Thomas is Harry's lover. At one point Harry deliberately plays that role, and some minor characters continue to give him a hard time about it.
Even later, after Molly becomes a main character, Harry also gets this with her. She's his apprentice in magic, after all, and it's something of a social norm for wizards to sleep with their apprentices.
In Firestar, Ned DuBois is so deeply estranged from his wife, Betsy, that neither of them gives a damn anymore. Which is why he spends every third page thinking about exactly how little she must give a shit that he's disappeared to Brazil, is sleeping with every woman who will let him, and hasn't yet finished his letter to her.
In The Great Gatsby, Nick apparently had a situation like this back at home, since he spent a lot of time hanging out with his female friend. Unlike most examples, she really wasn't his girlfriend — part of the reason he moved was because people were starting to gossip and expecting him to propose, which Nick didn't want to do. He claims it's all just gossip, but he makes a point to clearly break whatever it might've been off before getting together with Jordan.
Of course I knew what they were referring to, but I wasn't even vaguely engaged. The fact that gossip had published the banns was one of the reasons I had come East. You can't stop going with an old friend on account of rumors, and on the other hand I had no intentions of being rumored into marriage.
In Roger Zelazny's Lord of Light, Rudra declares that he never was romantically involved with Kali. The reason why he started hunting jackbirds after one of her lovers was incarnated as one was that he disliked their songs.
Simon towards Maureen in The Mortal Instruments, in whom he is genuinely not interested despite her liking him to an absurd degree. It comes back to bite him in the ass later on.
In On the Jellicoe Road, Taylor denies being Jonah Griggs' girlfriend, even though she is secretly in love with him (and they get together at the end anyway).
Gaspode: Your girlfriend… Victor: She's not my girlfriend! Gaspode: Would-be girlfriend…
Percy Jackson and the Olympians': In Battle of the Labyrinth, Percy makes it clear to his mother that his planned afternoon at the movies with Annabeth is not a date. Sally Jackson is not convinced. One gets the distinct impression that neither is Percy. And yes, he and Annabeth do become a couple, though not until a book later.
Rachel Griffin: In The Unexpected Enlightenment of Rachel Griffin, Rachel says this about Gaius. She has more than the usual excuse, since they only met the day previous and she feels the gap in their ages is too wide. Later, knowing him to be in danger, Rachel is upset because she hasn't really had a chance to consider whether she wants him as her boyfriend.
In Ravenscliff, Cecile inverts it saying "He's not my brother," meaning to her cheerleader friend that she has an option on her new stepbrother.
In Vision of the Future, an alien calls Mara Luke's "beloved companion," clearly misunderstanding their relationship. Then again, maybe not, since they get engaged at the end of the book. Also, in the same book, Mara reveals to Luke that she wasn't "involved" with Lando.
Death Star has Uli, a jaded surgeon who still pines after Bariss Offee, a Jedi Knight who was killed twenty years ago. He's summoned to tend to Leia after she is tortured. While talking to her, as she plants the idea that he should risk imprisonment and leave Imperial service, he's struck by her eyes, which are brown. Bariss's were blue. Talking to her even for that little space of time shakes him up, and he tells his companions about her. Later this leads to them referring to her as his girlfriend, and he delivers the Stock Phrase.
In the first book of Terry Goodkind's Sword of Truth series, Zedd is introduced to Kahlan by Richard... but not before Zedd calls out Richard for being rude by not introducing him to his "girlfriend." Richard calmly denies this, only for Zedd to joke about Richard, therefore, denying that Kahlan is a girl.
Twilight: Throughout most of Eclipse, Bella tries to convince everyone that Jacob is Not Her Boyfriend. Then she realizes that she does love him, but she loves Edward more, thus casting Jacob in the role of Unlucky Childhood Friend.
The Underland Chronicles': In Gregor and the Marks of Secret, Gregor and Luxa are going to investigate the Nibbler's situation, but since no one can know about it, they pretend that they are going on a picnic. Of course, Howard shows up and offers to join them, so Gregor, looking for an excuse, tells him that they're going on a date. Even when Howard finds out that Gregor was lying, he still chews him out because, seeing as Luxa's a princess and Gregor's not even an Underlander, they couldn't possibly be married. Gregor states several times that he and Luxa aren't like that and marriage is thinking way too far ahead, but then Howard asks Gregor why he thought Howard might believe it in the first place, rendering all his arguments useless.
Danny: She's my best friend, Max. She's been inside my head... that doesn't mean she's my girlfriend or something!
The War Against the Chtorr: In "A Matter for Men," McCarthy's Jerk Ass co-worker Ted deliberately lets an annoying officer think they're gay lovers to piss him off. McCarthy spends the rest of the novel denying that he and Ted are boyfriends, "or any other kind of friends."
Zero Sight: Dieter, when asked by Jules (Betty) if he and Rei (Veronica) had sex in front of the fireplace in Rei's cabin, denies it vehemently - much to the dismay of the rest of the students in the cafeteria, who had been eavesdropping.