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Happens in episode "Lisa the Vegetarian," when it was Lisa who did something bad for a change:
Marge: "Bart, Nooooo!" Bart:(Standing beside her) "What?" Marge: "Sorry, force of habit. Lisa, nooooo!"
In "Wedding For Disaster", Homer is kidnapped and Bart and Lisa, after finding a potential clue, assume Sideshow Bob is responsible. They track him down, but he is proven innocent of this particular crime. Ironically, one of the true culprits was a near-victim of Sideshow Bob in the past, Selma Bouvier, along with Patty.
Happens earlier in "Brother from Another Series" where Bob goes to work building a dam with his brother Cecil's company. Bart suspects Bob is up to no good as usual but this turns out to be the one time he isn't planning something evil, it's his brother in an embezzlement (and technically revenge) scheme. When Wiggum shows up to arrest Cecil, he arrests Bob as well, mostly just out of habit.
In the episode Two Dozen And One Greyhounds, Lisa, Marge, and Homer wonder who was causing various problems within the house lately (such as tearing up all her test papers, a broken vase, and spreading garbage all over the neighbor's yard before Homer got the chance to, respectively). Bart quips that he was this time innocent of these, and felt they were simply senseless destruction without any of his usual commentary. Turns out, it was the dog, who was continuing his path of destruction even in the room where they were located discussing what's happening.
Santa's Little Helper himself was implied to have this same trope applied to him in the same episode. When they discover some stuff buried underneath the house (specifically, Lisa's Bongo Drums, Bart's Strobelight, and Homer's "best of Ray Stevens featuring 'The Streak'" record) Homer guessed that it was the dog that buried all of their stuff. Marge's response to Homer implies that it was in fact she who buried at least one of the items that Santa's Little Helper uncovered.
Bart has been expelled from Springfield Elementary School twice. Ironically, both times it was for something that he didn't actually do.
In "The Seven-Beer Snitch," Fat Tony's mafia, while they are in prison, deduce that one of their fellow inmates was a rat, to which Johnny Tightlips points to Frankie the Squealer as the rat. However, not only does Johnny deny being the rat, but he also reminds him that he's actually the pigeon. It was Homer Simpson who was the rat.
In the Sushi Pack episode "The Thing That Wasn't There," an electrical creature that only Maguro can see is causing havoc all over the city. Since the attacks all have to do with electricity, the rest of the Pack assume that Unagi, the electric eel member of The Legion of Low Tide is up to no good. When they confront him, he denies having anything to do with it.
Unagi: "What'd I do? I didn't do anything!"
Kani: "Yeah, right."
Tako: "We're on to you, Unagi. Your plan."
Unagi: "Um, what plan was that?"
Ikura: "Your plan to distract everyone by turning up the volume on their car radios while you take over all the vacuum cleaners in Wharf City."
Unagi: "Hm... Not bad. But that isn't my plan. I don't have a plan. I wish I had a plan!"
In the episode which provides the page quote, the Gangreen Gang uses crank calls to fool the girls are into believing the series regular villains are doing something evil and confront them — only to find all three of them relaxing at home. Although the girls are not convinced, the villains quickly realize something is up and team up to deal with the pranksters themselves.
In another episode, a hit to the head makes Bubbles believe she is Mojo Jojo, stealing his clothes to match. The other girls instantly assume the latter is responsible, which leads to the priceless line:
Mojo Jojo: "You have got to be kidding. I'm wet, I'm naked, your sister is wearing my clothes, and this is all part of some evil plot TO RULE THE WORLD AS A SOGGY CHIMP IN MY BIRTHDAY SUIT?!"
Bubbles proceeded to beat up her sisters, get knocked on the head again by Mojo Jojo, wake up to see him standing over her sisters gloating, assume he did it and kick his ass for hurting her sisters.
Technically he did cause this (he hit her in the head), but by accident.
In Where on Earth Is Carmen Sandiego?, it often seems like the only time that the two protagonists Ivy and Zack actually do catch their nemesis Carmen is when she didn't do what they caught her for.
It plays with this one: When their Rusty and Brock get kidnapped (along with Baron Underbheit and Pete White), the titular characters immediately call the Monarch (more or less the Big Bad) to demand their release. He responds that it wasn't him this time, but "I have something planned for next week."
When Brock wakes up and finds himself chained in a dungeon with the other three, he immediately accuses Underbheit of being responsible, leading to this priceless response:
David Xanatos was behind so much of the troubles, that they assumed he was responsible for Goliath and Elisa's disappearance. Brooklyn opposed confronting him on it, as it would only tip him off. It did.
Talon: Drop the act, Xanatos. Where's Elisa?
Xanatos: I'm afraid I haven't seen her.
Broadway: Yeah right. Just like you haven't seen Goliath and Bronx.
This happens to him a few times. In another episode, where the Gargoyles are looking into who stole the Scrolls of Merlin, and Broadway is missing, they immediately head to Xanatos, only to have Owen tell them Xanatos had nothing to do with it. He then helpfully suggests they try MacBeth, who was behind the theft.
An interesting example in one episode, Sevarius and Xanatos create an evil clone of Goliath as an instrument in one of Xanatos' plans. A few weeks later, Sevarius recieves a message from the clone posing as Xanatos, telling him to steal several million dollars from Xanatos Enterprises and then meet Xanatos at an abandoned offshore oil rig. Sevarius does this without question, assuming it to be part of a "Machiavellian scheme against your (Xanatos') enemies", when Xanatos shows up and begins berating Sevarius for emebezzlement, his first assumption is that they're being watched.
Inverted in one episode of A Pup Named Scooby-Doo, where it turns out it really was Red Herring this time; naturally, it was the one episode where Freddie promised not to accuse of him of anything.
When she finds out that her Arch-Enemy Dr. Drakken has been broken out of prison by a woman with "green energy blasts", she naturally drops in on his sidekick Shego, only to find out later that it was actually an alien who did it.
Shego:I'm. On. Vacation! Ron: So, it wasn't you that busted out Drakken? Shego: Who do you think I'm vacationing from?
The same episode also had an inversion occur: In the scene Drakken was busted out of prison, the ceiling of his cell was blown up, and he initially thinks that its one of Shego's bailouts again. Another prisoner then reveals that the person in question is in fact trying to bust Drakken out.
Also done in the first part of the two-parter series finale: Graduation Part 1. When several golf courses were undergoing eruptions, Kim Possible suspects Duff Killigan for the event. When confronted with the issue, Killigan explains that he wasn't involved, and takes it a step further to reveal that his own golf course was defaced in a similar manner.
Ron and Yori attempt to track down their sensei in one episode when it is believed that Monkey Fist kidnapped him. Turns out, not only did Monkey Fist have absolutely nothing to do with the kidnapping, but the actual kidnapper, Gorilla Fist/ DNAmy actually kidnapped Sensei in order to deceive Ron and Yori into trying to track down Monkey Fist so she could locate him (since Monkey Fist was trying to flee from her).
A more minor example: In one episode, items were stolen from a shop. When Kim and Ron question the Storeowner of who robbed the store, he explains that one of them was burly. Knowing that this was Senor Senior Jr., Kim and Ron deduce naturally that his father was also involved in the robbery. The storeowner corrects them and states the other accomplice was actually a woman producing green flames, a description that matched Shego.
At the beginning of an episode of Buzz Lightyear of Star Command, a bunch of important politicians are kidnapped. Buzz then videocalls Zurg to confront him. Not only does Zurg claim he has nothing to do with it (calling it too obvious), he steps aside to show that he was in a meeting with every other recurring villain on the show who deny it as well. However, Zurg also mentions his "great plans for the next fiscal year".
One episode of Rugrats has Suzie blame Angelica for stealing her brand-new tricycle and punishes her by tying her doll to a balloon and letting it go. Despite the evidence against her, Angelica was completely innocent - Suzie's trike was under her porch, Angelica's trike was her own and Angelica's red hands (which Suzie thought was from opening her garage's painted doors) were actually from her finger painting an apology letter. Thankfully for Suzie, a miracle (or a low-flying plane) gets Angelica's doll back to her and everyone's happy again. Except for poor Chuckie, since it was his balloon tied to the doll. The lesson he learned that day was "Never let Suzie borrow your balloon".
In the Invader Zim episode "Planet Jackers", Zim initially thinks GIR is responsible for screwing up his telescope, but this turns out to not be the case.
Zim: You mean something's broken, and it's not your fault?
GIR: I know. I'm scared too!
Hurricanes played this trope in the episode "Target: Winston". When Stats reveals to Amanda Carey evidence suggesting that the explosion that almost killed Winston Honeychurch wasn't an accident, she quickly suspected that Stavros Garkos, the show's main Big Bad and Corrupt Corporate Executive, was behind this. She later learned he wasn't.
Robotnik: To be truthful, you horrible hedgehog, I have no idea where your feckless friend is. Sonic: And why should I believe you? Robotnik: Use your spiky head! If I'd had captured your companion, I'd be torturing him right now.
In Spider-Man: The New Animated Series, Kraven the Hunter apparently murders Mary Jane. In a rage, Spider-Man very nearly kills Kraven, only to discover that Kraven is innocent. Mary Jane was never murdered, and Spider-Man had been tricked by two other villains into thinking Kraven had killed her. (Kraven had killed the parents of the villains, and they weren't powerful enough to take revenge themselves.) Kraven doesn't get away scot-free, however: Spider-Man still drops him off with the police.
In Arthur, after Francine's bike was allegedly stolen, Muffy and the others suspected that Binky may have stolen the bike. During a meeting, Binky stormed over to Muffy and asked if she was the one who is accusing him of stealing her bike. After she confirms it, Binky then reveals, while looking timidly to the others, that he's innocent.
Hero example: in the Fantastic Four: World's Greatest Heroes episode "Frightful", the Frightful Four are damaging the FF's reputation. Since Johnny's already known to be careless with his powers, it's very hard for him to convince anyone he wasn't responsible for burning down a building ... especially as he has to keep specifiying "I did not burn down that building".
In "A Piniata Named Desire", Roger loses a part in a play to another person. When news hits that both the actress and her understudy were both killed and Roger is their replacement, Stan accuses Roger of killing them to get the part. Roger says that he didn't kill them, to which even he was surprised.
In the Batman: The Animated Series episode "Second Chance", Two-Face is kidnapped from the hospital before an operation to heal his scars (and hopefully restore Harvey Dent completely) can be done. At first, there are two suspects, Rupert Thorne (whose enmity with Two-Face goes back a long time) and the Penguin (who Two-Face had recently come to blows with) but both criminals give pretty convincing arguments for having nothing to do with it. As it turned out, Two-Face himself, or rather his evil personality, engineered his own kidnapping; as Batman tells him, "You're your own worst enemy, Harvey..."
Later, in The New Adventures of Batman, Batman and Robin intercept Scarecrow after he escaped from Arkham Asylum. However, he reveals while they have him in custody that he wasn't even planning to do any crimes. Actually, he broke out just to get away from Arkham Asylum due to the new security chief (who was extremely abusive to the prisoners).
In "Make 'Em Laugh," Batman and Robin discover the Mad Hatter's mind-control chips on people who inexplicably became ludicrous supervillains. Including the Mad Hatter himself—the Joker swiped them to exact revenge for being snubbed at a comedy competition.
In the episode "Knight Time", Supes and Robin discover that Bruce has fallen victim to Mind Control, so they track down Gotham's primary suspect—the Mad Hatter. However, after examining the evidence, the Hatter confesses that the technology used on Bruce is way too advanced to be of his own making and suggests an alien source—and true enough, it belonged to Brainiac.
In the episode "Solar Power", Lois was quick to suspect that Luminous has blocked off the sun's yellow rays to cripple Superman on Lex Luther's order, but Lex was equally quick to defend himself:
Lois: Come on, Lex! Those are your satellites up there, and Lightner’s worked for you before! How do you expect me to believe you have nothing to do with it?
Luther: What you believe makes little difference to me. The fact is, I did provide Lightner resources while behind bars, but only for legitimate LexCorp research. I had no idea he’d escape, and I certainly didn’t tell him to hijack my satellites for his own revenge.
Lois: Heck, why not? You’d love to see Superman dead.
Luther: Oh, please, Lois, forget that I’m losing millions in communications revenues, do you really think I’d jeopardize the welfare of the planet just to settle my personal grudge with Superman?
On Recess, Randall also had this trope invoked on him twice: The first time, most of the secrets that TJ and the others held were exposed to the teachers and staff, to which they ended up busted. They initially think Randall was behind their being ratted out, but Randall (who was in the garbage can to listen in) insisted that he did not. A chase to the bathroom later, and they end up discovering that Randall really wasn't behind their being ratted out that time: It was the so-called "cool kid" Stone who joined up with their posse who was in fact an undercover department of education individual who disguised himself as a student so Superintendent Skinner could find out the going abouts by the school who did it. The second time was when Randall hired the Ashleys' younger brothers, the Tylers, to act as proxies for him for his snitching job due to his getting cold at his sleuthing skills. One day, a lot more kids were put in The Box, including King Bob, whom he blamed Randall for it. However, Randall mentioned that reporting higher authority figures was a low even he wouldn't go as low as, and immediately told off the Ashleys' brothers for it, and attempted to put a stop to it, although they were one step ahead of him and reported him for it as well. Both instances also resulted in an Enemy Mine between Randall and the other kids.
Subverted on Tuff Puppy. The Chameleon frames Snaptrap for blowing up a building, and openly accuses him of such. Snaptrap, who has blown up many buildings and doesn't have a particularly good memory, assumes that this is one of the many crimes he is guilty of, and reacts by trying to kill both the Chameleon and Dudley. When Snaptrap finally remembers that he was out shopping at the time of the crime and innocent, he claims that he should not be arrested, since he was framed. Dudley retorts that Snaptrap still spent the episode attacking other characters, there's no such thing as Wrongful Accusation Insurance, and he can be sent to jail for these assaults.
The Life and Times of Juniper Lee: Ray Ray is so much of a troublemaker that it's hard for June to believe when he's innocent unless she is (or knows about) his alibi (then Dennis becomes main suspect by default). In fact, the two times Ray Ray invoked the trope had Dennis involved: breaking into June's room (Dennis and the two magical creatures that kidnapped him) and stealing a book from June (Dennis alone and Ray Ray protested he's not into books).
In Family Guy, after Chris is sent to a fat camp to lose weight, the other fat children are being killed off in the middle of the night one by one via strangulation. Everyone assumes Patrick, Lois' brother, did it because he was the town's "Fat Guy Strangler" several seasons back. Patrick says he had changed and had nothing to do with the murders at the camp. He even offers to help find the real killer, who turns out to be the former hot dog eating champion. He murdered every boy that had blonde hair because he remembered Chris having blonde hair and wanted to kill him in revenge for losing to him in the contest. The killer also had released Patrick from his insane asylum because he knew Patrick was the Fat Guy Strangler and everyone would naturally blame him once they hear he is loose. When the Griffins go to apologize to Patrick for the misunderstanding, he disappears.
An extreme example shows up in the third act of the Mr. Bogus episode "Bad Luck Bogus". After a blackout occurs in the neighborhood, Bogus suspects his sworn enemies, Ratty and Mole, to be the perpetrators of said blackout. However, when he confronts them, Ratty claims that he and Mole didn't have anything to do with the blackout. Of course, earlier, we saw that it was actually the evil Bogus clone that was responsible for the blackout, but Bogus just jumped to conclusions and assumed right off the bat that Ratty and Mole did it.
On an episode of Garfieldand Friends, Jon, Garfield and Odie are camping at a park. The ranger mentions that campers have been complaining about their lunches mysteriously disappearing over the last few weeks. Jon immediately glares at Garfield who says "Don't look at me. I just got here."
In the episode "The Patty Caper," a new shipment of the Krabby Patty secret ingredient arrived, but ends up missing, leaving Spongebob and Patrick to track it down. Naturally, their first suspect is Plankton, who, it just so happens, was making a Krabby Patty. However, as it turns out, he had nothing to do with it for once, and the Krabby Patty he made was his own version as part of a series of attempts to find out the secret ingredient himself. As it turns out, Mr. Krabs took the ingredient himself to avoid paying $1.98 for it, and he is forced to sell free Krabby Patties as punishment.
The episode "Best Frenemies" has Mr. Krabs losing business because of the new "Kelp Shake" that been selling well for a time. Naturally, Mr. Krabs confronted Planton about it, only to find he was about as surprised as Mr. Krabs was about the Kelp Shake making him lose business. They then joined together in a Enemy Mine situation (with Plankton's motivation being he wants to be the only one to defeat Mr. Krabs).
Seriously happened in an episode of Bravestarr. When the title character was missing, Thirty-Thirty assumed that Tex-Hex had kidnapped him (the fact that a local stool-pigeon told him that when he roughed the guy up, just to get away from him, helped), broke into the Hexagon, and nearly tore the place apart before he found out that Bravestarr had actually left to deal with another problem. (Ironically, the problem was that Sandstorm, one of Tex-Hex's goons, had decided to take his other henchmen to rob a caravan without asking Tex first. Not only did that start the whole problem, it left the Hexagon nearly undefended against the angry cyborg.) When the truth came out, Bravestarr actually made Thirty-Thirty apologize to Tex and offered to help clean up the place. (However, Tex was even angrier at Sandstorm for starting the whole thing by disobeying him, and said he would make him do it.)
In the Season 4 premiere of My Little Pony: Friendship Is Magic, Twilight Sparkle summons Discord, assuming he's behind the chaos caused by the Everfree Forest encroaching on Ponyville. He insists he had nothing to do with it, but can't resist tweaking the ponies' noses in the process.
Discord: Don't get me wrong, I absolutely love what you've done with the place, but I couldn't possibly take responsibility.
In fact he had just about everything to do with it. He planted the seeds of the plot (literally) back before he was sealed in stone for the first time, though he didn't specifically make them start growing, they grew on their own. He does point them in the general direction of the threat, but justifies not telling them its exact nature because it would spoil all the nice character development that would come of finding it themselves.
Subverted in "Teela's Triumph". Skeletor developed a ray that sends people to another dimension and tested it on a falcon. Unbeknownst to him, the falcon was the Sorceress so, when He-Man accused Skeletor of being responsible for her disappearance, He-Man was right but Skeletor didn't know.
In a non-villainous example, in Teenage Mutant Ninja Turtles (2012), a news report mentions a "half-man, half-reptile, and all-angry" creature attacking a man in the sewers. All eyes turn to Raphael, who insists it wasn't him. (It was Leatherhead.)