Marvel Knights: Spider-Man kick off with a story where aunt May gets kidnapped and he goes running to Norman Osborn, who's in prison, demanding he return her. Osborn says he had nothing to do with it, what with, you know, being in prison and all...
This is actually remarkably Genre Savvy on Spidey's part, since being in prison or even dead has not stopped Osborn from wreaking all sorts of havoc in Peter's life before.
This happens to Spider-Man a LOT, apparently. During the Fallen Son arc mourning Captain America's death. While at the grave of Uncle Ben, Spidey 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.
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 on 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 a recent Batman issue, Batman pursues a recently escaped Joker because he thinks Joker was responsible for attacking and poisoning Commissioner Gordon's 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.
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.