John is thrown into what looks very much like Earth, and immediately suspects Scorpius of messing with his head. However, when he finds Scorpius in the simulacrum, he protests that he's not the one doing it this time.
Happens a whole bunch in season 4 when Scorpius joins our heroes on Moya and then again in "The Peacekeeper Wars."
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.
In the Deep Space Nine episode Who Mourns For Morn when one of the title character's former fellow gang members asks the others which one killed him none of them have a clue who did it. Turns out nobody did.
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.
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, their subsequent handling of the situation leads to her not bothering to be The Atoner anymore.
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.