In the third season of Alias, Sydney suspects recurring villains Arvin Sloane and Mr. Sark of being the masterminds behind her abduction and subsequent Laser-Guided Amnesia leading up to the Time Skip, and accuses Sloane in particular of being the secret mastermind behind the Covenant. As it turns out, he and Sark are totally innocent of involvement and, in fact, the amnesia was self-inflicted.
In Arrow, after Sara is murdered, Nyssa immediately concludes it was Malcolm Merlyn. After a three-way fight between the two of them and Oliver, Malcolm insists that while he is a mass-murderer he is not guilty of this. Oliver believes him immediately and actually places him under protection from the League of Assassins (smoothly ignoring the aforementioned mass-murder), to Nyssa's utter disgust as she remains convinced he was the one who did it. He technically did it by using Thea as a patsy through the use of a psychedelic drug that made her commit the murder. it turns out to be part of a grand scheme to become the new leader of the League of Assassins.
Happens in quite a few episodes of Bewitched. Darrin usually assumes that his troubles are being caused by his wicked mother-in-law, Endora, who claims to be innocent (or doesn't appear in the episode at all). It turns out to be someone else was screwing with Darrin, or the problem was completely mundane with no magic involved.
Breaking Bad: Out of everything that Walter White did over the course of the series, killing Hank was not one of them. Unfortunately, his wife and son are already done with him at this point, immediately assume he did it, and refuse to hear him out.
Not a recurring Big Bad, but in one episode of Columbo the killers try to make it look like a repeat offender did their murder. Columbo doesn't seem convinced but pays a visit to that offender to be sure.
Offender: Who are you? Columbo: Lieutenant Columbo. Homicide. Offender: Homicide... no, I haven't done one of those recently.
He then makes Columbo a cup of tea and explains how he would have done it if it were him. His method would have involved less finesse and more explosives.
In "A Well Respected Man", Amanda and Nolan confront Datak suspecting him of abducting Kenya. Datak denies it, as it was apparently too subtle. For bonus points, he practically confesses to the murder of Elah Bandik.
Datak: When I wish to send a message, I rarely leave it unsigned. It's hubris plain and simple. A character flaw, but one my wife seems to enjoy.
He gets it again in "If You Could See Her Through My Eyes", Stahma thinks Datak paid Favi Kurr to boycott Stahma's businesses. He however points out Favi Kurr is far too noble to be bribed, and he wasn't involved in this.
The entire Tarr family gets this in "Doll Parts", with all three assuming one of them must have been responsible for Deidre Lamb's murder. Both Datak and Stahma end up agreeing that their son Alak wouldn't have the guts to do it, and Stahma bursts out laughing when she realizes it was their sweet and innocent daughter-in-law, Christie.
"The Five Doctors": When the Third Doctor and Sarah Jane Smith stumble upon the Master in the Death Zone on Gallifrey, the Doctor naturally surmises that he's the one responsible for their banishment here, but the Master protests he's, for once, innocent. In fact, he's been sent by the Time Lords High Council to rescue the five incarnations of the Doctor.
"Bad Wolf"/"The Parting of the Ways": After the Daleks have been revealed as behind the Gamestation's killergame shows, and have been manipulating Earth's society for centuries, the Doctor assumes that they must, therefore, also be responsible for the "Bad Wolf" Arc Words that have been popping up all season. The Dalek Emperor, when confronted about this, denies responsibility, and the Doctor realizes that if the Emperor, who has a serious god complex, had spread the words, he would have gloated about it like he did the rest of his plans. The Arc Words were, in fact, spread by the temporarily empowered Rose as the Physical God Bad Wolf.
"Army of Ghosts"/"Doomsday": After the titular "Army of Ghosts" is revealed to be an invading Cyberman army from the parallel "Pete'sWorld", following the appearance of a mysterious "void ship" in the basement of government institute Torchwood, the Doctor assumes that the Cybermen had something to do with the void ship. However, the Cyber-Leader reveals that they had merely followed the void ship through the breach in realities, and that they were not responsible for the ship's creation. The ship turns out to have been housing the Cult of Skaro, a highly secretive group of Daleks.
On one episode of Dracula: The Series, the title vampire encounters the heroes in a crypt when the casket opens. A minor character climbs out and reveals that he was turned into a vampire. Dracula replies "Don't look at me. He's not my type."
Drake & Josh: When Mrs. Hayfer finds her convertible parked in the middle of her classroom, she immediately accuses Drake of being the one who put it there. Drake protests that he's not responsible for this, despite the fact that his sweater is found in the car and having a history of elaborate pranks. Doesn't help that she has a vocal and self-admitted hatred for Drake. It eventually turns out it wasn't Drake, but perfect student Mindy, who was outraged that Mrs. Hayfer had daredgive her a B grade on a test. Upon this revelation, Mrs. Hayfer apologizes to Drake (very reluctantly), but immediately declares this changes nothing about her hatred of him.
Inverted in Drop the Dead Donkey after Damien has sabotaged the dinner where Helen introduces her girlfriend to her colleagues Joy stages an accident in the resulting confusion.
Damien: ... and then you "accidentally" hit me in the face, five times? Henry: No, one of them was me and you deserved it.
A non-villainous example in Elementary: When Watson's boyfriend Andrew gets an offer of a job in Copenhagen, Watson is convinced that it's a ploy by Sherlock to get rid of him. Sherlock rightly insists he's innocent, telling Watson he likes Andrew even though they didn't hit it off initially, and has no reason to get rid of him.
Played straight in the first season. Sherlock believes that Irene Adler was murdered by a Serial Killer known as "M." due to the circumstances of her death matching M.'s very specific method of killing. When he finally tracks M., aka Sebastian Moran, down Moran claims he couldn't have killed Adler as he was doing six months in prison for an unrelated assault charge at the time which Sherlock is able to confirm by contacting the prison.
In Family Matters, an explosion happens in the high school chemistry lab, and Urkel is nearby. Urkel is blamed but protests innocence. The Winslows actually believe and defend him, since they know that while Urkel is very disaster-prone, he has never once denied involvement in one of his accidents. It was another student trying to frame Urkel.
Another episode has Steve believing that he's being the target of a criminal, stating that he saw a face peeking into his bedroom window late at night. Upon stating this, everybody turns to Myra, who immediately claims; "I stopped doing that a while ago."
Fargo Season Four: Josto Fadda has done some really bad things throughout the season including ordering the murder of a child and scheming to have his brother killed by a rival gang. He is then accused of setting up the murder of his own father, the previous Don. The audience knows that he is innocent of that crime but there is strong evidence against him and the other mobsters do not believe his protestations. Josto has stepped over the line so much that no one who can save him believes that he did not do it this time.
John suddenly wakes up on Earth, with everybody claiming he was just in a coma since the pilot episode. Though he has many suspects (The Ancients, Maldis, Delvians...), he zeroes in on Scorpius when he finds that, aside from the Scorpius playing the drums (It Makes Sense in Context, actually no it doesn't) there's a second Scorpius only he can see. But Scorpius protests his innocence, and he's telling the truth.
Happens a whole bunch of times in season 4 after Scorpius joins our heroes on Moya; John initially blames everything on him. Happens again in "The Peacekeeper Wars".
The very first scene in Game of Thrones has Cersei and Jaime Lannister discussing Jon Arryn's death, and though it's not obvious until later their conversation is essentially this. Several characters in-story conclude that the Lannisters killed him (the Lannisters do have a good reason to want Jon Arryn dead) but this all turns out to be a Red Herring and the real culprit is Arryn's own wife Lysa and Littlefinger, who framed the Lannisters. It makes sense too, the Lannisters are in essentially as commanding a power position as you can possibly imagine, and the ensuing War of the Five Kings destabilizes the Kingdom, the exact opposite of what the ruling faction would want. Even when the information Jon Arryn had does comes out anyways (that Cerci's children belong to Jamie, not Robert) it's basically irrelevant in terms of larger scale impact.
In the episode "Ho'opa'i", undercover cop Reggie Williams and his family are attacked and his wife killed after his cover inside mobster Jimmy Cannon's organization is blown. Cannon of course denies any involvement; Williams goes rogue and swears revenge, but comes to believe Cannon is telling the truth. It turns out it was Cannon's son acting without his father's knowledge.
In "Na hala a ka makua", a man named Roy Parrish convicted of murder escapes while being transported to prison and forces McGarrett and Williams at gunpoint to help him clear his name. He admits his guilt over a bank robbery for which he'd served his time and claims he was chosen as a patsy for that reason. He's able to clear his name, but is killed by the real killers in the process.
In the Hercules: The Legendary Journeys episode "Hercules on Trial", Hercules is Arrested for Heroism. Ares visits him in his cell to gloat, but when he is accused of setting this up, he clarifies that he had done nothing and the humans arrested him on their own.
In the episode "5 To 9", when it's discovered that someone's been altering shipments to the pharmacy to steal meds, Dr. Cuddy's first question is...
Cuddy: Was it the whole shipment or just one med? Oscar: Just one. Cuddy: Vicodin? Oscar: No, pseudoephedrin tablets.
The thief turns out to be a lab tech running a meth lab. Recovering (at the time) Vicodin addict Dr. House had nothing to do with it.
Wilson once won a prank war with House in Season 2 by filing halfway through his cane, causing him to collapse in the hallway. The same thing happens in the same hallway in Season 3.
Wilson:[deadpan] Not me this time. House: I know! It's your damn dog! He chews on everything!
When House and Wilson move into their new condo in Season 6, each accuses the other of pulling the latest series of pranks on him, and each insists he didn't do it this time. House eventually comes to suspect every one of his employees, who all have reasons to hate him, and it turns out to be Cuddy's new boyfriend Lucas.
Subverted when Foreman accuses House of pretending to be him and cancelling his job interview. House denies it and accuses Cuddy, who accuses Wilson, who accuses Cameron. They eventually figure out that it really was House and he wanted them "chasing ghosts".
In the first episode of The InBESTigators, after a montage of times that Kyle was responsible for Ezra getting hit in the head with a ball, prompting an angry "Kyle!", the present day smack turns out to be someone else's fault and Kyle is quite indignant to be blamed.
Happens with Kyle again in "The Case of the Unhappy Camper", when his pranking antics get him fingered for stealing the principal's phone, sticking it in the rice and damaging it; it was someone else entirely.
Japanese Police ProceduralKochira Hon-Ikegamisho had a number of reformed criminal characters who would often be questioned following crimes that resembled their earlier ones.
One episode of Law & Order: Special Victims Unit has Casey Novak attacked while working the case of a serial rapist. Benson and Stabler initially suspect the same man who they're already looking at for the rapes, but while he does turn out to be the rapist, it turns out he had nothing to do with the assault on Casey; she was attacked by the brother of one of the victims in the case, who was angry at Casey for getting his sister involved in the case because it meant that people would find out she's not a virgin, and he sees that as shameful and doesn't want anyone to know.
In another episode, two daughters from a traditional Christian family are raped, and the detectives suspect their oldest brother, who turns out to have a history of sexual assault. However, while the brother clearly has issues that need to be (and haven't been) addressed, he didn't rape his sisters; it was the family pastor.
The episode "Quarry" the remains of a long dead child are found, and it is believed he was the victim of a serial rapist and murderer on death row (set to be executed soon). When confronted about it, he denies having anything to do with it. He confesses to multiple other children, but insists this one was not him. He had nothing to do with this murder, one of his many victims is responsible.
On Limitless a bomber admits that he is the notorious bombmaker/contract killer they've been looking for, and he planned on killing the journalist whose supposed car accident the FBI is investigating but he didn't do it. It was a legitimate car accident which took place before the planned assassination point caused by the victim having a stroke caused by an engineered virus he'd been exposed to, a virus meant for someone else.
In The Mentalist, a serial abductor/killer, known as the balloon killer, was suspected of kidnapping a child. However, after shooting him, he implies (and Jane confirms via phone and a note) that this time, he's innocent.
Detective: What [were you arrested] for? Crow:[as suspect] Crossbow killing... but I had nothing to do with this one!
In one episode of NCIS, Tony is framed for a crime. One of the first people he suspects is Ziva.
Ziva: I would never do that! Tony:[looks at her] Ziva: Alright, I could. But I didn't.
The NCIS: Los Angeles episode "Exit Strategy" had the NCIS team thinking that the Sudanese dictator Khaled was responsible for the attempted assassination of Jada, his sister who had defected to America in his previous appearance, as he had the strong motive of keeping her silent in regards to his abuse of human rights in the region. However, when they contact him, he denies the attempt on his sister's life, citing that even he would not harm family, although the NCIS doesn't buy it. Turns out, the actual party responsible for the attempted assassination (or at least the one most directly responsible) was the CEO of an international French company that was also involved in Khaled's dictatorship, as Jada's exposure of Khaled's human rights abuses would also result in an investigation on their company and result in a tribunal against them, with France as a country also potentially getting into deep trouble.
Ned's Declassified School Survival Guide: Loomer is accused of vandalism and protests that he's innocent, even while admitting he doesn't know what he's being accused of. Ned notes that when you regularly lie to the teachers, they won't believe you when you're actually telling the truth.
In "The Cricket Game", someone has framed Regina for Archie's murder. Emma, Snow, and Charming conclude that Gold is responsible and storm into his shop.
Gold: Nice to see your memory's still intact, dearie, but, this time, I'm afraid I'm going to have to disappoint you. It wasn't me.
By extension, this applies to Regina as well. She really was innocent and was genuinely trying to change, but no one is willing to believe it. Unfortunately, it gives Cora the opportunity take advantage to the situation
Again in season three Regina is blamed for reenacting the curse when it wasn't her, it was Snow, in order to return to Storybrooke and find Emma in order to defeat Zelena. She says outright that she's as clueless as any of them.
In season six, Belle is dosed with magic that speeds up her pregnancy and everyone assumes Gold did it, since he had pretty compelling motivation to — Belle was going to keep their child away from him but changing the game would give him the opportunity to abduct the child. He wasn't involved at all. In fact, he even figures out who the real culprit is while no one else is even looking for another suspect, but he doesn't bother protesting his innocence or trying to convince anyone who did do it because he knows no one will believe him.
In the Vampire Diaries spin-off The Originals, Klaus, main character and alternatively Anti-Hero or Anti-Villain depending on the episode, faces this when Tyler Lockwood shows up and suggests that Klaus might be willing to use his unborn baby to create an army of hybrid vampire/werewolves, which he tried to do before with someone else's blood. Klaus is outraged that his own brother would even suspect him of this, even given his known habit of being a bastard.
Subverted on Overhaulin. The show once relieved a mark of both her daily driver and her work truck and tricked out both. At the end, they presented her with her customized work truck, but claimed they had nothing to do with her daily driver's theft. After she went to get ready for a photo shoot, they brought out her customized daily driver.
In The Pinkertons episode "Mudd and Clay", Jeremiah Mudd is accused of a still fire that killed 13 people, with the only question being whether the fire was deliberate or an accident caused by gross negligence. Mudd insists that he's innocent; he builds his stills to last, and he found evidence that the fire was caused by sabotage. He's telling the truth.
In "Pariah", people start getting viciously assaulted from behind in locked rooms and other enclosed spaces. Everyone accuses Alicia Baker, as she can teleport and is a previously established psycho. Alicia protests that she has been cured of her insanity, and in fact, has an alibi for one of the attempts - she was with the town sheriff. Eventually, Alicia gets assaulted and killed by the real culprit, Tim Westcott, a man with Super Strength and the ability to transform into living sand, which was how he entered those locked rooms. When Clark found out, he wasn't happy...
"Sneeze": Lex believes Lionel is the one that's having someone follow him, and doesn't believe when Lionel assures that it isn't.
"Kara": Lex is fully certain that he didn't set up the bomb in Lana's car, but bides his time in prison until Lionel sets up a fall guy.
"Veritas": Lionel tells Chloe he didn't kill Patricia. But of course, she doesn't believe him, as he also killed Patricia's father.
In the episode "Firstborn", Lursa and B'Etor of the House of Duras are suspected of an assasination attempt against Worf. It turns out a future version of Alexander, Worf's son, had traveled back in time to stage this attempt so as to motivate the young Alexander to become a Klingon warrior.
The episode "Timescape" has a variation of this. Picard, Troi, Data, and La Forge are returning from a conference and encounter the Enterprise and a Romulan vessel, apparently frozen in a temporal field. At first, it looks very much like the two ships are fighting and the Romulans have both attacked and boarded the Enterprise, a suspicion that is only strengthened when they investigate the inside of the ship and find that Riker is unconscious, and worse, Dr. Crusher has been shot at close-range by a Romulan soldier (the temporal freezing the only reason she likely survives). Eventually, after a way to reverse the temporal freezing is discovered, the more complicated truth emerges: The Enterprise was responding to a distress call from the Romulan vessel and helping them evacuate the ship, the true culprits in the case being shapeshifting aliens posing as Romulans. (The soldier had tried to fire on one of the imposters; Crusher had simply gotten in the way.)
In "True Q," Q creates a couple of imminent disasters on the Enterprise to test the powers of Amanda Rogers. When a disaster occurs later on the planet below, Picard asks if it's Q's doing, but he replies "Not this time, Picard" and vanishes.
Moseby fell victim of a prank and blamed Zack, who denied it, saying it wasn't his style and mentioning things he usually does. When the real culprit was revealed to be AlexRusso, Zack expected Moseby to apologize but Moseby instead pointed out Zack had previously confessed to pranks he had yet to be punished for.
When Zack is accused of stealing jewellery, Moseby comes to his defense with a massively backhanded endorsement of his character, reciting a long list of Zack's character flaws before finally concluding "but he is not a thief". That may technically be true, but he did attempt to steal hotel towels from Jesse McCartney's room in The Suite Life of Zack and Cody.
In another episode Moseby believes that Zack is responsible for cracking a window and flooding a bar. Moseby is proven wrong when a friend of Zack shows that he helped him film a music video at the time the window broke.
In Suits, when a rival firm steals associates from Pearson Hardman, Jessica and Harvey understandably but incorrectly assume Louis is helping them. By this point, Louis has eroded Harvey's trust so much from his actual transgressions that Harvey doesn't care whether or not Louis is guilty of this one.
In The Vampire Diaries, season 3 has the council getting mysteriously blown up at the end of its first episode. Next episode, both the Sheriff and Elena go to ask Damon if he did it... much to his irritation, since for once, he has nothing to do with that.
In The Wire, a warrant is issued for the arrest of Omar. A delivery driver was shot in cold blood, and the only witness fingered him. Omar has a towering reputation for violence among gangsters and police, but a few cops more familiar with his methods are skeptical. Det. McNulty allows him a phone call as he's arrested that probably saves his life, and Det. Bunk Moreland pisses off his colleagues in Homicide trying to get them to investigate deeper. The truth is that the witness lied as part of a frame-up. Since Omar's profession is robbing drug dealers, one of the drug bosses framed him with the intent of getting him shivved in lock-up.
Det. Moreland: This here is a taxpayer murder with an eyeball witness. Omar: The eyeball witness is lying, yo. Come on, now. When have you ever known me to put my gun on anybody that wasn't in the game?
In The X-Files episode "Aubrey", evidence links two violent crimes to a man who served decades for similar crimes. He doesn't pretend to have been rehabilitated in the slightest, instead offering in his defense the fact that he's in his eighties and can't go anywhere without an oxygen tank.