Sgt. Frog has a rather sad example in one chapter. Keroro is expecting praise for doing a good job cleaning the house, but is instead met with furious accusations by Natsumi and Fuyuki of screwing with computer networks across the city, and has a nervous breakdown when they refuse to believe his pleas that he's not responsible. The real culprits turn out to be the Garuru Platoon, as a prelude to taking over the invasion of Earth.
Subverted in Naruto, when Tobi claims that he was not behind the Kyuubi attacking Konoha despite confirming or expanding on much of what Sasuke was told about him. A later flashback arc shows that he really was.
Actually played straight, he stated that the Uchiha Clan wasn't behind it. This is correct. They had no knowledge of it as he acted alone.
Pokémon has its share of villains that aren't Team Rocket, whether single-episode Pokemon menaces, thieves, the region's local villainous team, or Bill and Cassidy. As Jessie and James end up appearing in nearly every episode, they get more than their share of this trope.
Subverted in the first season of Rosario + Vampire; in Chapter 27, Tsukune gets a centipedia sent after him. Although his current problem (the monstrels) are not shown in that chapter themselves, he does suspect that his 'centipede thing' opponent is allied with them. He's wrong: Headmaster Exorcist Mikogami sent him after Tsukune to test his ghoul powers and damn did it work.
In a non-villainous version, the first plotline in Haiyore! Nyarko-san W has two aliens ransack the Great Celaeno Library looking for a forbidden book. Mahiro suspects that they wanted Nyarko's overdue library book, because she (unwittingly) tends to be behind these events. When it turns out that he had the book they wantednote he was looking at it while in the library and shoved it into his jacket pocket without thinking with the aliens attacked, he gives a Big "NO!" and Nyarko says that it was unfair for him to instantly assume it was her.
Happens twice in Death Note. The first time, a man connected with the Kira investigation gets a (survivable) heart attack simply from the stress of the job; the second time, it's someone else running around with a Death Note supporting Kira's aims.
In Cross Ange, Ange blames a lot of things that Hilda did to her while she was at Arzenal and thus she can't trust her. As part of her Arson, Murder, and Jaywalking accusations, one of said accusations was that the Perolina costume stinks, something Hilda never did. Ersha was the one wearing the costume, handing out the balloons before Ange stole it. Hilda even calls her out on that one.
In Touhou Ibarakasen ~ Wild and Horned Hermit, someone has been attacking the people at the Myoren Temple, and Reimu is the first suspect not only because of the religious rivalry between the two shrines but because she's been kicking more Yokai butt than usual lately. When confronted, Reimu insists that it wasn't her and points out that if she had done it, she'd be bragging about it (since it would improve her standing with the human village). The culprit was actually Suika, using her density manipulation powers to prank the temple for not paying proper respects to her when they set up near Yokai Mountain.
In an episode of Cardcaptor Sakura, Kero attempts to convince Sakura and Tomo that Spinel Sun, not him, was the one who ate all of the school festival's sweets.
Fairy Tail: The Fiore Royal Family blames Zeref for Acnologia, convinced the former transformed the latter into a dragon. While Zeref is responsible for nearly every major event in series and a lot of strife in the characters' backstories (either due to his research and creations, people's desire to attain his power, and/or ironically his plan to defeat Acnologia), he is not responsible for Acnologia. Acnologia's transformation was actually a natural consequence of the use of Dragon Slaying magic — if anyone is to blame for him becoming the Black Dragon of the Apocalypse, it'd be Spriggan 12 member Irene Belserion, who created Dragon Slaying magic.