Marvel Knights: Spider-Man kicks off with a story in which Aunt May is kidnapped. Spider-Man immediately confronts Norman Osborn, who's in prison, demanding he return her. Osborn says he had nothing to do with it, because he's in prison. Of course, being imprisoned (or even dead) has not stopped Osborn on other occasions. And it turns out that he really was responsible.
This happens to Spider-Man a lot, apparently. During the 'Fallen Son' arc, Peter visits Uncle Ben's grave and sees Rhino walking through the cemetery. He attacks, thinking he's up to something (despite Rhino pleading that he isn't here to fight), and their fight breaks a gravestone belonging to Rhino's mother... which was the only reason he was there in the first place. When he realizes this, Spider-Man attempts to apologize, but Rhino is, understandably, far too angry to listen.
In the Spider-Man spin off Jackpot, the heroine, later accompanied by Spidey himself, beats up a minor villainess who was smuggling but really hadn't anything to do with what Jackpot wanted to know about. The snippy answer of the villainess was something around the lines of: "What? Do you think every villain in New York gets a daily update about every crime?!"
Similarly, there was a comic where a series of crimes is commited that seem to be the work of the Phantom Blot. Mickey goes to see him in jail, but the Blot tells him he's in jail and hasn't busted out, as the guards will testify, but he appreciates Mickey thinking of him.
In another comic, Mickey and O'Hara are investigating some robberies when they run into the Blot walking down the street, prompting the latter to arrest him on the spot (with no evidence whatsoever). The Blot doesn't resist and firmly denies everything, which Mickey notices is not like him and thinks he may even be innocent. It turns out he did do it... however he's not actually the Phantom Blot but rather a magically summoned duplicate created by Magica DeSpell.
With the Blot it seems to be a recurring theme. Due to him wearing disguises anyway, it is easy for various copycats to use his identity and general style for a while. There are several variations on how is this resolved. At least some having the genuine Blot being the one to take down the imitators.
Also, there's the problem that Phantom Blot that being in jail has not stopped him from committing crimes, like the time he had a ring that accelerated his subjective time (effectively making him go into Bullet Time) that he would keep outside the window in case the police searched his cell, allowing him to break out, commit his crime and come back to his cell without anyone noticing.
In one issue of Birds of Prey, Black Canary's old mentor was murdered while she visited him in Hong Kong, even though he was terminally ill and would have died soon anyway. She quickly assumed that the supervillainess Cheshire committed the crime due to their history of animosity; the means of the crime, poison, also happened to be Cheshire's specialty. After Black Canary tracked Cheshire down, attacked and captured her, she found out that Cheshire did not do it; rather, it was the deed of a corrupt US senator who arranged the murder specifically so it would point to Cheshire. The two of them were enemies and he hoped Canary would deal with Cheshire for him. However, they eventually discover that it really was Cheshire after all. She made it look like she was being framed so that Canary would help her get back to the US as part of a Gambit Roulette.
A story in Gotham Central had someone killing teenagers dressed as Robin, but despite Batman's violent interrogations, none of the usual rogues turned out to have any involvement.
In Arkham Asylum: Living Hell, Dr. Arkham cannot bring himself to admit a gaggle of demons tried to open a portal to Hell in the Asylum, being a Flat-Earth Atheist. So instead he reasons the Scarecrow released fear gas in the vents and has him thrown in solitary for a month. Scarecrow sputters a Big "WHAT?!". Not that anyone believes him.
The Astro City story "Adventures In Other Worlds" plays this to eleven. When Astra Furst of the First Family goes missing, they hunt down all of their usual super-villain enemies, convinced that one of them has captured her. Each villain's latest scheme gets disrupted, even though none of them are guilty of kidnapping Astra... who, instead, has run away from home to experience elementary school (and learn how to play hopscotch).
In an issue of the Justice League Unlimited spin-off comic, The Question sets out to discover who was responsible for a bomb smuggled into the Watchtower. Lex Luthor is the lead suspect, but when confronted Luthor points out that if the bomb had gone off as planned, the Justice League would never have known what hit them — and when he destroys the Justice League, he'll do it in such a way that they'll know exactly what hit them.
Joker: Stop me if you've heard this one before... I'm innocent.
"Joker: Devil's Advocate" is another example of this: the Joker was actually innocent of the crime of placing Joker venom on lickable stamps. Turns out it was a disgruntled member of the Post Office who did it to frame the Joker, who killed his wife.
In Batman The Black Mirror, Batman pursues a recently escaped Joker because he thinks Joker was responsible for attacking and poisoning Commissioner Gordon's ex-wife. After defeating him, however, and Batman tells him to stay away from the Gordons, Joker revealed that this time, he was completely innocent of attacking the Gordons. It was actually James Gordon Jr. who did the deed.
Joker has made a point of telling Batman that if it was him, he'd certainly let him know.
In Asterix and Son, the title character demands to know if the local Roman commander recognizes a baby left of on Asterix' doorstep.
"I've recognized seventeen children waiting for me back in Rome, but I'm quite sure that one's not mine."
In Star Wars: Legacy, the Yuuzhan Vong were accused of using the terraforming to devastate the already damaged planets ecosystems even further by causing deformities in the terraforming process, an accusation that stemmed from their role in the Yuuzhan Vong conflict long ago. The Yuuzhan Vong protested that they were in fact innocent and that they did not cause the deformities, at least not deliberately, to which the Jedi believed them. Turns out, they really were innocent: The One Sith sabotaged the terraforming project with the help of a Yuuzhan Vong plant of theirs who wanted revenge for their defeat.
Just before the Our Worlds at War Mega-Crossover over at DC, Superman is tussling with General Zod in the upper atmosphere, when a huge SOMETHING flies past Superman, towards the Earth. Supe's response?
Superman: You missed! Zod: ... That wasn't mine. Superman: I'm not falling for— Zod: No, listen, to me. That wasn't mine. (they stare at each other) Perhaps this is best settled later?
In Curtis, Greg and Diane Wilkins are in their bedroom for the night, only to hear a crash originating from Curtis and Barry's room. They naturally assume that they got into a fight again. However, the final panel has them screaming for help with multiple crashing sounds, revealing that this time, the crash was not from one of their fights.
The next strip reveals the cause for the crash were hailstones the size of eggs or golfballs.
In The Sandman, Dream gets dumped by his most recent girlfriend. Afterwards, he goes to see his brother / sister Desire, who has a history of setting up and destroying any kind of relationship on a multi-universal scale. Desire bluntly tells him that "it" would love to take credit for Dream getting dumped, but "it" had nothing to do with the situation; this time it was all Dream's fault.
In one of the children's book tie-ins of The Flash, the Weather Wizard is released to a halfway house on the same day a tornado rips through the city; naturally, everyone assumes he did it, but the Flash uses his science skills to deduce that the tornado began before he could have regained access to his weather control wand. In the end, it's suggested that—as per the comics—he no longer quite needs the wand.
In Identity Crisis, none of the supervillains had anything to do with Sue Dibny's death.
Inverted with Grand Moff Trachta in Star Wars: Darth Vader and the Ghost Prison. When Trachta is spotted by Vader and Tohm near the ailing Emperor Palpatine, they immediately accuse him of being involved in Gentis' coup against the Emperor. Trachta vehemently denies any involvement in the coup. In case anyone is wondering exactly how this qualifies as an inversion, Ghost Prison takes place chronology-wise a good 17 years before Star Wars Empire: Betrayal, where Trachta definitely was involved in a Military Coup, and in fact instigated that particular coup.
Barry Allen/The Flash went gunning for his nemesis Professor Zoom when Barry believes that Zoom was responsible for the Flashpoint timeline. Professor Zoom was only indirectly responsible, when he killed Barry's mother via time travel. It was Barry preventing that murder that actually started Flashpoint.
The Transformers: Windblade: Windblade believes Starscream has been sabotaging, Metroplex's power, set up a bomb to kill her, and has been mining the living citybot for resources. While Starscream is guilty of the last crime, he justifies it saying Metroplex is a big bot and can handle it, and instead accuses her of the sabotage and power failures all in an attempt to undermine his rule. It turns out he was sincere in his belief that the attempt on her life was merely a maintenance problem caused by her, and there really is another force at play that's been behind Metroplex's problems.
Marvel's one-shot all-humor issue The Fantastic Four Roast (February, 1982) has a mysterious figure out to do in the FF during the titular testimonial. Ben "The Thing" Grimm suspects it's Doctor Doom, who approaches the dias and bellows "WRONG, CAMEL BREATH!!"
Dr. Doom: Dr. Doom, Dr. Doom, Dr. Doom. Why does everyone always suspect that Dr. Doom is the culprit?
Human Torch: Well, it sure isn't Soupy Sales, tin head!
Similar to the TV episode "Telephonies," The Powerpuff Girls story "Mojo's Day Off" (which was unpublished) dealt with calamities striking Townsville, and the girls automatically suspect it's Mojo Jojo each time. Mojo is fatigued and is trying to relax, only for the girls to burst into his lair to accuse him of each calamity.
"Meet The Micros" (issue #65) was the story that introduced the Micro-Puffs, tiny sprite-like avatars of the girls. Only instead of doing good, these girls are quite mischievous. After winning over their friendship, the Micro-Puffs make the girls think that Mojo Jojo, Him and Fuzzy Lumpkins are committing crimes. It turns out they weren't as the girls find out the hard way.
Warlord of Mars: One story arc involved the Green Martians suddenly becoming more violent than usual, placing the planet's newfound stability in peril. The scheming and treacherousWhite Martians are naturally the heroes' first suspects. However, after further investigation, its revealed that the real culprits behind it are the Yellow Martians of Okara, specifically the ones thought to be the heroes' allies.
One Daredevil storyline had Mr. Hyde contact Matt Murdock and demand he defend him, as while Hyde is a known killer and was planning on killing the victim, someone else beat him to it.
The Superman arc "Dead Again" is all about this. When a Superman corpse shows up and seems to suggest that this was the real Superman still dead from his fight with Doomsday and the current hero is only a fake who thinks he's the real Superman, the Man of Steel begins searching throughout his Rogues Gallery, including Luthor, Mxyzptlk, Brainiac, and Darkseid, to see who could be behind the hoax, with each one of his enemies revealing they have an alibi for what's happened. It's eventually revealed that Brainiac was only faking innocence and really was the mastermind of the whole thing.