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 Nine-Tailed Fox 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 put it in his jacket pocket without thinking, he gives a Big "NO!" and Nyarko lightly scolds him for immediately blaming 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.