In Artemis Fowl: The Arctic Incident, Holly and Root assume it's Artemis behind the B'wa Kell goblin smugglings, but after they kidnap him to find out, it turns out not to be the case.
In the second Night of the Living Dummy book, the heroine, her sister, and her parents enter the sister's room to find that all her bedroom walls have been graffiti'd. The mother yells at the youngest brother, a notorious prankster, but he stops her by saying that this time he's innocent, and that this is messed-up even for him. It turns out that Slappy did it, but who'd believe that?
Harry and Ron use Polyjuice potion Chamber of Secrets to imitate Crabbe and Goyle, Draco Malfoy's two mooks, in the hopes of getting Draco to admit that he's the heir of Slytherin, and thus the cause of all the shenanigans happening at Hogwarts that year. Instead, they hear Draco ranting about how thrilled he is that it's happening and how he'd love to congratulate whoever is actually behind it.
Similarly, in the film version of Harry Potter and the Prisoner of Azkaban, Ron initially guesses when there is a long line towards the Fat Lady that Neville Longbottom must have forgotten the password again, only to learn from Neville's exclamation that he was behind Ron the whole time, and thus couldn't have been the one keeping them out of the common room. It's revealed shortly afterwards that the reason they aren't allowed access is because the Fat Lady was scared away from her painting.
In Harry Potter and the Goblet of Fire, Snape blames Harry's trio for stealing the Polyjuice Potion ingredients missing from his stores. Although they were guilty of that 2 books ago, they are not responsible for it this time — Barty Crouch is. Since Snape didn't mention when the ingredients were stolen, Harry thought he was talking about the original theft, so he was simply lying that he wasn't behind it.
Also in The Goblet of Fire, after Filch is again the victim of one of Peeves' practical jokes, he finds Harry's golden egg, recognizes it as something belonging to one of the Triwizard Tournament contestants, and quickly accuses Peeves of stealing. Actually, Harry had simply dropped it while sneaking around with his cloak of invisibility while figuring out a clue. Peeves quickly makes himself scarce, and Snape - who is all-too-often the Straight Man to Filch - convinces the caretaker to forget about it. (Of course, Filch would likely have taken any opportunity to pin something serious on Peeves, given how much of a headache the guy often caused him.)
Fainne says this exact line in Child of the Prophecy, by Juliet Mariller. It's really her grandmother who happens to have similar powers and much more motive...
A variation in Death Masks. Early in the story, one of Marcone's hitters attacks Harry and a priest who's coming to Harry for a job. Later on, when Harry confronts Marcone about it, Marcone blinks in surprise. While Marcone did order the hit, it turns out it wasn't a hit on Harry at all, but on the Denarian-in-disguise priest.
Happens again with Nicodemus in Small Favor. When Nicodemus is talking about the Black Council as an enemy of his, Harry says he already knows that Nicodemus is in cahoots with them, as Hellfire was used in a Black Council attack during Proven Guilty. Nicodemus's reaction is pure shock, as he apparently had no idea about it, indicating that someone in his own faction is betraying him.
Minor character Mortimer Lundquist isn't a recurring villain, but his specialty in magic (talking to ghosts) is considered borderline against the law of magic concerning Necromancy, so the Wardens have spoken to him in the past about not crossing that line. The first few times Harry goes to him for information, Morty starts by saying he hasn't done anything.
Simon Heap in Darke has a hard time convincing Septimus and Sir Hereward that he isn't to blame for the Darke Domaine.
In Black Legion, the Inquisition accuses Khayon of wide variety of war crimes and atrocities. While he doesn't deny that he committed multiple genocides, he takes his time pointing out just what he wasn't responsible for.
Albrecht Detweiler's centuries-long conspiracy to destroy the Kingdom of Manticore and Republic of Haven — among others — is responsible for pretty much every bad thing that has happened in the history of the two star kingdoms, going back centuries. When the leaders of those two star nations find this out, they're justifiably and incandescently angry and immediately begin making plans to vaporize him into subatomic particles, meanwhile laying any number of charges at his door. Those charges are all very accurate — except for the one about Arnold Giancola.
Benjamin: In fact, they're busy telling the Manty Parliament — and, I'm sure, the Havenite Congress and all the rest of the fucking galaxy! — all about the Mesan plan to conquer the known universe. In fact, you'll be astonished to know that Secretary of State Arnold Giancola was in the nefarious Alignment's pay when he deliberately maneuvered Haven back into shooting at the Manties! Albrecht: What? (blinks in surprise) We didn't have anything to do with that!
Soon I Will Be Invincible: Dr. Impossible has escaped from prison for the thirteenth time and his heroic nemesis Corefire is missing. Could these two incidents possibly be unrelated? As it turns out... yes, much to Dr. Impossible's annoyance.
In Last Sacrifice, Rose asks Victor Dashkov if he had anything to do with the murder of Queen Tatiana Ivashkov. He replies negatively and adds "I have much more sophisticated methods to accomplish my goals".
In While My Pretty One Sleeps by Mary Higgins Clark, Mafia boss Nicky Sepetti, who's about to be sent to prison, makes a threatening remark to Police Commissioner Myles Kearny about how his wife and daughter might need some protection. When Myles's wife Renata is murdered less than two months later, everyone naturally assumes that Sepetti was behind it. He denies this until the day he dies (literally), but the police and Renata's family are not convinced. It turns out Renata's murder was completely unrelated to the Mafia; she was designing a glamorous fashion line and a designer she knew killed her so he could steal her ideas.
Zadie Smith of Reconstructing Amelia does some truly horrific things over the course of the novel. She hazes all new members of her clique, bullies everyone, including her best friend, cheats, drinks heavily, manipulates everyone around her, outs Amelia as a lesbian against her will, becoming the ringleader in a school-wide hazing session, but in spite of all that, she did notkill Amelia. That was actually Sylvia.
In Dora Wilk Series, a fertility witch notorious for less-than-legal spells vehemently denies turning three muggles into toads, and even points Dora and Witkacy at the real perpetrator.
The Hunger Games: When confronted with the deaths of the children who made up his 'human shield', Snow reveals that he had absolutely nothing to do with it, and it was President Coin who did the deed. Likewise, Gale denies knowing if the plan was formed from one of his ideas, but by this point Katniss has lost what little ability she had left to take people at their word.
Þrymskviða in Poetic Edda has it in the beginning. When Thor's hammer disappears, he immediately tells Loki in no uncertain terms that stealing the hammer would be the last straw for everyone if proved. Only Loki wasn't behind it this time.
The second The Girl from the Miracles District book opens with Nikita being poisoned right after a meeting with her Archnemesis Mom. She calls her mother and tells her that she knows Irena did it - to Irena's absolute surprise, as she didn't even know something's happened to her daughter.
The Lannisters are guilty of many, many things, but they haven't murdered Jon Arryn. They are accused of that early into the first book, and Tyrion tries to deny it during his trial in the Eyrie. Nobody believes him, thanks to the family's reputation and the fact the real murderess is in charge of the trial and playing a Wounded Gazelle Gambit.
Sandor Clegane readily admits to being a killer, but you'd better not accuse him of crimes committed by his brother. His "not me this time" can be very violent.
In The Trials of Apollo of the Riordanverse, Apollo claims he did not flay Marsyas alive for claiming to be a better musician than him, but let the story spread because he liked the attention. Apollo, like most gods, is an unreliable narrator, but notably he confesses to plenty of other, similar moments of god wrath and unpleasantries, so it is likely he truly means it.
In the Diogenes Club story "Cold Snap", the director of a weather research station attempts to wipe out the human race with an engineered ice age. The research station is owned by the Diabolical Mastermind Derek Leech, the Greater-Scope Villain of the series, who insists that he has nothing to do with the director's plot and had no idea the man had a private agenda. He's telling the truth: The director is just so boring that nobody involved in hiring him could pay attention to him long enough to realize what he was up to. (However, that doesn't mean that Leech is averse to taking advantage of the situation now that he's been alerted to it...)
Defied in Shadow of the Conqueror.Daylen knows that he's blamed for multitudes of crimes that he never committed, but isn't interested in clearing things up, as almost everyone considers him Beyond Redemption, anyway. During his trial at the end, he even pleads guilty to all the crimes he never committed.