The Hitler Rants videos on YouTube normally sees either Fegelein or Himmler (or often both) pulling antics on Hitler. Once the spin-off series based around Joseph Stalin and the cast of Das Boot got their own antic masters, Fegelein frequently had to explain to Hitler's staff that he wasn't involved in whatever embarassment had just befallen Hitler, often with little success.
In the version of Hellsing Ultimate Abridged by Team Four Star, Alucard is a JerkassSociopathic HeroBlood Knight who is basically the logical result of what would happen if you gave the biggest Troll on the Internet unstoppable superpowers. So when he's involved in an incident with the police in Brazil, Integra's first assumption is that it's his fault and she calls bullshit when Alucard protests that he was just minding his own business until the police turned up and started shooting. Alucard is being entirely honest — he hadn't done a thing (yet) to get his door kicked in by SWAT. They were actually bribed by the villains into attacking him. It probably didn't help that he greeted them with Your Mom, though.
In 'The Camping Webisode' of DSBT InsaniT, Koden tells Alex and Seth not to beat up Andy for Frets, Martha asks 'why', and Koden, knowing Alex is the one to say stuff like that, does a Double Take when he realizes it didn't come from him for once.
In one Global Guardians story set during the 9/11 attacks, Achilles immediately contacts his father, the Evil Overlord known as Lord Doom. The first word's out of Doom's mouth are "Don't even think of accusing me or anyone who works for me of committing such a vile and cowardly act," before Achilles can say anything to the man.
Gaea, a known Manipulative Bastard, has a video that is very copromising for her faction's top player end up on her blog. It took a solid alibi to convince her own Guild Master that she had gotten framed.
The actual poster of the video later got this, mostly due to happening to be in the same faction as the female player that had just broken one of the male protagonist's heart. On a side note, part of the audience was suspecting said female player to be working for him all along up to that point.
In Atop the Fourth Wall, both Linkara and the audience assume it was Mechakara who broke the Continuity Alarm. However, when he's finally confronted, he admits he didn't do it. As it turns out, it was Linksano who broke it.
Despite being the Token Evil Teammate for Hat Films, there are occasions when Smiffy's Pyro Maniac tendencies get him blamed for fires he didn't actually start. One example is in Minecraft 1.8.2 XBLA #5, when Ross accidentally places lava inside their (partially wooden) house, setting it on fire. Trott immediately shifts the blame to Smith, due to his habit of burning down their houses. He was similarly accused of stealing items, causing them to actually kill him... only to be stunned to not find them in his dropped inventory. Turns out they just missed them among all the junk in the chest.
During Cornerstone, the group (mainly Rythian) assume that Smiffy and someone else are posing as creepers to try and scare the others, after Smiffy has tried it before and died for his trouble. It turns out that no, those are actual creepers. Sjin also kills the wrong person for stealing his jetpack.
During Sips' Garry's ModMurder! series, Ross of Hat Films becomes The Dreaded as the murderer due to his shouting "EAT SHIT" at the top of his lungs. In at least one case, however, he's mistaken for the murderer as his efforts to shout "EAT SHIT" and put them off fail, resulting in him dying and everyone else assuming it's him.
In mashed's Omnileaks animated short, Winston, Mercy, Lucio, Tracer, Zarya, Genji, and Reaper capture Sombre, convinced that she leaked embarrassing secrets about them (the titular Omnileaks). Sombre is thoroughly confused by the accusations, but admits that she wished she had leaked the info after hearing the hilarious Leaks.note It's hinted to have been Doomfist, but given that Winston's passwords are ALL "password", it could have been anyone.