The Writing On The Wall features Adventurer ArchaeologistDaring Do exploring an Ancient Tomb surrounded by metal thorns, with a room full of writing in dozens of long-lost languages. Daring Do believes that the eponymous writing is the same as in every other such edifice she has explored: nothing more than false warnings of a curse intended to scare away superstitious tomb robbers. She is absolutely right that the message is intended to scare away tomb robbers. Unfortunately for her, she's wrong about what the message actually is - a warning about the building's true contents. She's not in an adventure story, but a Horror story, and what is inside the building is genuinely dangerous to her.
In Transformers Meta, Barricade had successfully deduced that Bumblebee had been trying to trick him into letting him go by lying about finding mermaids which would grant him wishes, but still fully believed that mermaids were real and declared he would "find them by himself."
He proceeded to list the things he would wish for upon his success.
Skeleton: WHAT IS THE WIND SPEED OF A SWELLOW? Phanphy: Wait! I saw this on TV once! I know the answer! Is it a Hoennese Swellow or an Orrean Swellow? Skeleton: HOENNESE. Phanphy: No, you were supposed to say you didn't know, then fall off a cliff. Skeleton: YOU WATCH TOO MUCH TV.
In the Naruto fic "A Few Angry Words" Pain seems to think he's Julius Caesar marching into Rome. He's more like the Antichrist marching into the Jezreel Valley.
It's still not entirely certain who's rightGenre Savvy in Harry Potter and the Methods of Rationality, but we know Draco isn't the Chessmaster he thinks he is, and Hermione does not in fact seem to be in a romantic comedy. Smart money's on Dumbledore's being wrong that it's a fantasy, and Harry may not actually be right that it's sci-fi (at least not the sort of sci-fi he thinks it is.)
We Just Want to Help You by Jeanne Hedge is a fic where a random fan of Bubblegum Crisis finds herself in the Tokyo of 2035, hurries over to offer to help Ms. Stingray... and gets tranqed and sent to the loony bin when it turns out she's not actually inBubblegum Crisis, but a relatively close (but significantly divergent) Alternate Dimension.
Later on, the crew goes to help a village that is being attacked by amoral mercenaries. The entire scenario seems like a classic Western tale where the heroes protect the helpless against an enemy with overwhelming firepower. In reality, they're in a psychic horror story involving a Town with a Dark Secret where everyone is being mind-controlled by an unstable telepath.
In With Strings Attached, in the second part of the Vasyn quest, the four find themselves in what they think is a hollow world/spaceship a la "For the World Is Hollow and I Have Touched the Sky". Given what they've already been through, this doesn't scare them, and they figure they know how to proceed. And then they find out they've actually been shrunk and put into a science experiment in someone's basement. That scares them.
Team 9 is full of idiots, though, and they are also misinformed about what is actually going on. Yukari, though, has no excuse, as she seems convinced, against all evidence, that she actually can take on Rin Satsuki, who already defeated her, Reimu, Eirin and some of Gensokyo's other powerhouses and possesses the power of a freakin' ARCHANGEL OF DEATH. Oh, and she apparently doesn't have any problems in trying to screw things over while she already has to deal with Yuuka, who placed a bounty on Rin Satsuki's head. If she had actually spent TWO SECONDS listening to what Eirin said, or, failing even that, had tried to find a peaceful solution, she wouldn't have ended playing Yuuka's game. If Rin actually WAS the Omnicidal Maniac she believes her to be, Gensokyo would have been ANNHILATED by now.
In Ultimate Sleepwalker: The New Dreams, the Ax-CrazyPsycho for Hire Bullseye revels in his supposed A-list status and looks down on C-List Fodder like the billiards-based 8-Ball. When they're hired by rival crime bosses who are fighting a Mob War, Bullseye and 8-Ball end up fighting. The cocky Bullseye thinks that, as the A-lister, he'll have an easy time against the C-list 8-Ball. However, Bullseye ends up impaled by a huge piece of metal and gets his head severed and knocked into a garbage can by 8-Ball, just to add insult to injury.
In Game Theory, Nanoha seems to think that she's in a standard magical girl show, that she can win fights by implementing crazy plans and improvising new spells without understanding how the magic works, and that it's okay to risk putting a lot of people in danger for the sake of one person. Thisisnotthecase.
In the Ben 10Fan FicHero High series, Ben seems to think of himself as a comic book hero who will defeat the bad guy and save the world. Instead he helps the bad guy to save the world and said guy gets off Scott free from his crimes. Also many of the Original Characters seemed to be driven to show Ben that he has a case of Wrong Genre Savvy.
In the A Certain Magical Index fic Wintertime, when Kagun Kihara accidentally walks in on Marian Slingeneyer bathing in a lake, he steals her clothes, thinking this will give him power over her. She coldly informs him that she is a Dvergr, not a swan maiden or selkie. He was lucky she decided not to kill him.
In Perfection Is Overrated, Midori, like in Mai-HiME, realizes that the conflict the Himes are involved with is not quite like the animes she's used to, although she learns to adjust, and mostly keeps her team together. The SUEs are largely driven by the belief that everything will go their way just like in fics in which they are the main character, not realizing that their actions are considered unreasonable and immoral by most people's standards, or that they will lead to their downfall.
Kyoko in the Puella Magi Madoka MagicaFan FicHave Your Cake And Eat It, after dying and going to the the afterlife for magical girls created by Madoka, makes the assumption that like in the anime series she's from, their is a more sinister meaning behind this seemingly innocent realm. Normally she'd be right, except she didn't realize she originated from a series where it is possible for idealism to win out, which is the line of thinking the Fan Fic is based around and as such, there is no sinister scheme behind anything.
In Hivefled, Lereal thinks that when Karkat and the trolls arrive, it's a clear sign that since the descendants of major rebels have arrived, it's time to take on the oppressors. And to be fair, there are a lot of stories where that would be true, but unfortunately, Lereal hasn't realised that it's not his story, it's Gamzee's, and the Sufferist rebellion is merely a backdrop- and so when Lereal takes the cultists to rise up against the oppressors, they all get slaughtered horribly, excepting one ship of mutineers and Karkat's ship.
When Dave arrives at St Lobaf in Brainbent, he acts as though he's in some kind of political drama or crime show- having been removed from his home because it was a terrible place to raise a child and his brother was a very unfit parent, he refuses to say anything, believing that if he talks about his life, it will be used against his brother in the upcoming hearing. After a while, he realises that he's in a dramedy, and more specifically, the hospital is genuinely trying to help him.
Shinji in RE-TAKE assumes he's in a Peggy SueFix Fic where most of the Evangelion series was All Just a Dream that showed him the future and his knowledge of the future can easily prevent all the problems that occurred in the regular series. He's dead wrong, as his actions to save Asuka lead to Rei committing suicide. Later he finds that what he saw was no dream, it was real memories and his actually possessing the Shinji of an alternate timeline without realizing it.
In Harry Potter and the Natural 20, Milo, a young wizard and adventurer from Dungeons & Dragons, is sent to the Harry Potter verse. Despite the different rules of magic and society, he treats everything as if he were still on a Dungeons & Dragons campaign, and always expects everything to follow Dungeons & Dragons rules.
In Our Queen Has Met Her Doom, Eridan thinks himself the protagonist of an old-fashioned romance novel: that he's the brave warrior who wins the beautiful princess's hand, that she will forgive him anything because she loves him, and that his romantic rival is villainous and pathetic. He couldn't be more wrong.
You saw parades and portraits and grand balls and grand battles and a beautiful love and a history that would last forever, but what you got was a chainsaw to the torso.
Sasuke assumes that Naruto was Obfuscating Stupidity all his time at the Academy. He recalls how many of Naruto's pranks and failures at the Academy would take out Chunin and that Naruto would say he was "joking" and assumes that Naruto graduated the first chance he got. He is wrong, as Naruto was genuinely joking and passed on accident.
Sakura assumes Naruto killed Iwa Genin simply because they prevented him becoming a Chunin when they in fact maimed and/or killed his teammates and is under the impression Naruto is due for a psychotic break due to his extreme irritability, restlessness and snappishness when he is forced to work with her.
Mizuko Sanbashi, a Kiri nin who was a proctor for the Kiri Chunin Exams was able to deduce with limited evidence that Naruto was the Kyuubi Jinchuriki, but believes that Naruto's parents died protecting him from the Yondaime to stop him from taking their son. In FT:TT, he believes that Naruto and his team were on a mission to get rid of an upstart ninja village (rather than stumbling into the scenario), covering it up by hiring Zabuza and his cohorts.
All the villages assume when Sarutobi is enacting an education reform and allowing past Genin-candidates to retake the exam that Konoha is re-militarizing.
Ra's Al Ghul is the only one to realize a connection between Alexander Harris and The Leviathan in A Spark of Genius. After realizing that Sparkbucks coffee (a franchise that supplies 100% of the world's coffee products and over 90% of the world's caffeine) is run out of a small Montana town that Xander owns and uses the same teleporter technology as The Leviathan to transport it's goods, he naturally assumes that Xander is funding The Leviathan in exchange for using his teleporter technology. In reality, Xander, The Leviathan, and the Grey Knight (allegedly The Leviathan's demon hunting cousin) are all the same person.
There's also the character of Inkwell from the Calm Before the Storm side story. He starts off as an aspiring Intrepid Reporter who thinks his work with the Ponies for the Ethical Treatment of Newfoals (PETN) will make him into some kind of brave whistleblower that will bring about change and better living conditions to the newfoals living in the Solar Empire. But not only does he discover that the real picture is far murkier (namely that the newfoals aren't being abused so much as TCB!Equestria is very dreadfully unprepared to support such an enormous population boom, and to say nothing of how the newfoals are the definition of Extreme Doormats and what the potion does to their minds), but his digging around for answers also ends up getting him into some very deep trouble with the authorities.