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."
In 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.
In the Star Trek: The Next Generation 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.)
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.
Japanese Police ProceduralKochira Hon-Ikegamisho had a number of reformed criminal characters who would often be questioned following crimes that resembled their earlier ones.
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.
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.
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.
Crow: (as suspect) "Crossbow killing...but I had nothing to do with this one!"
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."
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.
In the Smallville episode "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 was with her husband, Clark Kent, the whole time. 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...
Suite Life on Deck: 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.
Pair Of Kings: It was hard to believe Brady and Boomer weren't the ones to blow up the castle.
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 theorize and conclude that the Lannisters killed him (especially since they had a very good reason to want him dead) but this all turns out to be a Red Herring and the real culprit is actually Arryn's own wife Lysa and Littlefinger.
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.
Once Upon a Time: 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 in tact, 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 the House 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.
Oscar: No, pseudoephedrin tablets.
The thief turns out to be a lab tech running a meth lab and former (at the time) Vicodin-addict Dr. House wasn't even involved at all.
Wilson once won a prank war with House in Season 2 by filing half-way 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 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.
Doctor Who: In "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.
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.
In the Hawaii Five-0 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.