The final chapter of Batman: A Death In The Family has The Joker appointed ambassador to the United Nations by the Iranian government; the Iranians, who are Always Chaotic Evil in this story, plot to have the Clown Prince of Crime kill the U.N. General Assembly by gassing them right after making a speech. But Superman thwarts Joker's plan, causing the villain to flee the chamber with Batman in hot pursuit. The Joker hitches a ride on a helicopter with his gun-toting Iranian cronies, but Batman grabs hold of the aircraft just as it takes off and fights his way in to confront the cowering Joker. One of the Iranian gunmen panics and opens fire with his assault rifle. The result? It's bad enough that the gunman succeeds only in "harmlessly" nicking Batman's arm, but he also "manages" to deal a fatal wound to every person on board but Batman - including the pilot himself, whom he shoots in the back of the head! We are told that "the gunman immediately realizes his mistake," but he doesn't have long to regret it: Batman punches him out, knocking him unconscious and then diving into New York Harbor, leaving everyone in the chopper to die when it crashes into a nearby dock. (Well, except The Joker.)
Non-comedic example: In Secret Six, Black Alice admits that she tried to use Raven's powers to remove her father's asthma. She gave him cancer instead.
In one issue of X-MenStorm had one of these when it comes to dealing with her claustrophobia. The thing that set her off wasn't being trapped in rubble, having to fight in a small room, or anything like that. The villain was making threats against them, and used the word "tomb." Storm proceeded to flip. out., and spent multiple issues of the fight cowering in a corner. He wasn't even trying to prey on her phobia, he was just talking to them and accidentally incapacitated her.
When Storm finally managed to pull herself together and fight, her first attack sends a lightning bolt at The Juggernaut, which bounces off of him and strikes her, knocking her unconscious and back out of the fight. Despite the fact that Storm is immune to the effects of lightning.
Also from the X-Men, Juggernaut once became even more unstoppable with the power of another evil god. The X-Men try to stop him, trying ever grander plans that all fail epically (one of them is getting a guy who can ignite a person's blood to try it on him. The result? The unstoppable Juggernaut is now unstoppable and able to set anything he touches on fire.)
Happens to members of Spider-Man's rogues gallery whenever their Villain Decay is played for laughs but Lightmaster takes the cake: in one appearance, he announces his appearance in front of the Wall-crawler, then immediately gets knocked out with a falling duffel bag full of money.
How did One Moment in Time explain Spider-Man missing his own wedding? A fat man fell on him and he couldn't get him off. No, really. It becomes a lot worse once you remember that Spidey has Super Strength and should logically be capable of pushing off the man with ease— he's seen at one point throwing a car at somebody. One of his most iconic moments has him lifting a multi-ton piece of machinery off of him in order to save his Aunt May.
W.I.T.C.H. gives us Orube's attempt at learning how to cook: she somehow set the water of the pasta on fire!
Transformers: More than Meets the Eye: The rogue Decepticon team are being attacked by the Decepticon Justice Division, 5 Cons, who kill failures cowards and deserters. Krok is grabbed by two of them, Vos and Kaon, and Misfire comes to his aid... by accidentally shooting him 3 times in the chest. In addition, Vos and Kaon are taller, and Vos was standing between him and Krok.
One better. So Fort Max has snapped, locked himself, Rung, and Whirl in Rung's office and is threatening to kill them both. It comes down to an attempt to take out Fort Max from across the way by Swerve. He shoots... and blows Rung's head up.
In My Little Pony Micro Series Issue #3 once she learns about the hippies' predicament, Rarity does her best to get sure the production of "Goops for Stuff" is maximised to it's limit, to get sure the product remains 100% natural, is made in a way that nobody gets it's hooves dirty anymore and most important, not even a drop of it is wasted. She also gives the product a complete makeover to make it more attractive, and finally instructs the hippies about how to sell their products on a more efficient (and profitable) way so they could save their farm. After all of that hard work, the hippies and Rarity proceed to accidentally scare off their only potential customer.
In an early Lucky Luke comic, the Dalton brothers (the historical ones, not their horribly incompetent cousins) show off their ignorance by attempting to divide 10000 by 4 when sharing their loot and turning the simple operation into a complex mathematical formula with square roots and integrals.
Natasha: Clint. Clint: I know— Natasha: You have the army after you and no health and you're falling out of a crashing airplane. Clint: I know, Nat— Natasha: It's a bass fishing simulator, Clint. Clint: I know! It just— It just happens!