Shinji Ikari in Rebuild of Evangelion 3.0: after he wakes up from being extracted from Unit-01, everyone treats him with intense dislike and barely acknowledges his existence, leading to him wondering just what is going on that's making everyone act that way. It isn't until halfway through the movie that he gets an answer: his actions at the end of the last movie inadvertently caused Third Impact, and although Kaworu stopped the Impact before its completion, the world still pretty much died. The survivors have been living in a post-apocalyptic wasteland for the past 14 years because of what he did, and they've lost all sympathy they once had for him.
Ed Byrne joked in Pedantic And Whimsical that women in general have an annoying habit of instead of telling their boyfriend/husband what they did wrong, they'll just "acted pissed off" and let the man guess what he's done. So after the man has asked what he's done wrong, the woman will hit him with the line:
"'If you don't know what you've done, there's no point in me telling you.' What? You know it doesn't make any sense. Where's the logic in that statement? [...] It's like saying 'If you haven't eaten, there's no point in us making any dinner'."
In Terminator 2, the heroes track down the guy who'll invent the chip which leads to the Robot War in the future, and Sarah immediately tries to kill him in front of his family, even though he hasn't finished his research (much less known what would come of it). He calls her out on this after the situation's explained, but agrees to help destroy his work.
In A Christmas Story, after Ralphie's punishment for swearing, he must tell his mother where he heard the word. Not wanting to tell the truth that it was his dad, he blames the school bully. Ralphie's mom informs the kid's mother and we hear that kid being smacked and asking "What did I do?" coming from the other end of the phone.
In The Empire Strikes Back, Han and Chewbacca are being tortured by Vader (Han by electricity and Chewie by sound), and think it's just petty revenge since they weren't asked any questions. Vader was counting on Luke psychically sensing their torture and coming to rescue them.
In Oldboy the protagonist is kidnapped and held in a private prison. When released, he spends the rest of the movie trying to track down who did this to him and why.
In John C. Wright's The Golden Oecumene, Ungannis tries to invoke this trope by splitting herself into many personalities, some of whom would try erasing memories of her crimes, and still be executed for them. This is not greeted with horror by the Transcedence mass mind — legally, you can not evade punishment unless you rework your personality into a new person, and none of the split personalities had tried to redact the beliefs that had led Ungannis to commit the crime.
One of the most important points of Franz Kafka's The Trial is that the reader is never let in on the charge against the protagonist.
At this period of their Quarrel I entered the Library and was, as you may imagine, equally offended as Sophia at the ill-grounded Accusations of the malevolent and contemptible Macdonald.
One Sherlock Holmes story featured a young man, arrested for the murder of his father, showing no surprise and saying he deserved it. Watson thinks it proves guilt — an innocent man would have had this trope. Holmes counter-argues that the man had to know the strength of the evidence against him, and since he raised his hand against his father he may have regarded his arrest as just.
In the first Harry Potter book, the Dursleys punish Harry for causing magical things to happen. Since they never told him he was a wizard, Harry just thinks that weird things inexplicably happen around him and doesn't understand why they're considered his fault.
In King Rat, the main character denies the king his throne back, for reasons that any human would agree with but a rat could likely never understand.
Pretty much any incarnation of The Count of Monte Cristo features this. Edmond has no idea why he's imprisoned, until many years have passed in Chateau D'if.
Aviendha is subject to this type of punishment by the Wise Ones for much of book twelve of The Wheel of Time. She is ordered to do useless labour, which is the ultimate insult in the Aiel culture where even prisoners from enemy clans (gai'shain) are put to useful work. It turns out that she is meant to complain rather than stoically bearing it. This shows the strength of character necessary to become a Wise One.
In The Dark Half, the killer George Stark has the same fingerprints as novelist Thad Beaumont. Sheriff Pangborn arrives at Thad's house to arrest him, and his first clue that Thad isn't the killer is that Thad is utterly confused by the arrest. Pangborn has been a cop long enough to know that criminals who know they're guilty just don't act like that.
Live Action TV
Poor Gale has no idea what hit him in the Breaking Bad third season finale.
The Invisible Man: After the Official is badly beaten Darien is bewildered when Hobbes attacks him, points a gun at him and starts ranting at him. Hobbes has assumed Darien did it while suffering from Quicksilver madness.
El Chavo del ocho: Doña Florinda usually slaps Don Ramón for things that weren't his fault. There were occasions he doesn't even know what she's faulting him for.
Averted in Babylon 5, where a Mind Wiped serial killer turned mild-mannered monk has his memories forcibly returned to him, because the people hunting him down want to make damn sure he knows why they're after him.
In the Half-Quake series of Mods for Half-Life, the strange people(?) behind the scenes of the bizarre, punishing world the player character finds himself in claim that he deserves their torture simply for the "crime" of being human. But as a number of areas seem to be designed to showcase or even glorify sadism, the protagonist- and others- are given weapons so that they can survive longer (and therefore prolong their own suffering), and the grisly deaths of the victims are apparently televised for the entertainment of others, the possibility exists that they're simply rationalizing their own sick enjoyment.
Franziska von Karma of Ace Attorney fame likes to whip people for reasons which may or may not be valid. At least once, she whipped Phoenix instead of the actual target.
The South Park episode "Proper Condom Use" has some of this, wherein Cartman shows the other boys how to "milk a dog". Stan shows this off to his parents in front of company without knowing what he's doing, which results in this.
Sharon Marsh: Stanley, do you know why you're being grounded for 10 months?!
One episode of The Simpsons has Homer strangling Bart when he learns he needs to go attend to other matters. He orders Bart to think about what he's done since he can't carry out the full punishment. Bart has no idea why Homer was strangling him, and it turns out that Homer doesn't know what Bart did wrong either.
Attempts to teach small children and animals how to behave are at risk of falling foul of this trope if the time between the misdeed and the scolding is too long. Instead of correcting the misbehavior, this can actually make it worse by creating stress and confusion.