John Siegenthaler, a very respected journalist who signed onto That Other Wiki with the greatest of intentions, but singlehandedly ended up ruining it FOREVER. In May of 2005, some anonymous loser added some false information to his page that said that he was a suspect in John F. Kennedy's assassination. This error went unnoticed for five months. Then, someone informed Siegenthaler of the error. He created an account on Wikipedia to correct it, but the administrators didn't realize his intentions and kept reverting his corrections; they eventually blocked him. Also, by editing the article, he was in violation of the Wiki's Conflict of Interest guidelines, which specifically prohibit people from editing articles about themselves or people close to themselves. Eventually, a shitstorm went down that led to the creation of several controversial Wiki policies, including Biographies of Living Persons, the Oversight feature (and its very first use was on the Siegenthaler article!), and registration being required to start new articles. Most haters of Wikipedia say this was when the wiki Jumped the Shark. And all John Siegenthaler wanted to do was correct an error. Nice job breaking it, hero!
Ironically, Wikipedia Watch, a site that Wikipedia is at war with due to its webmaster posting personally identifying information about its editors, ended up being the hero in this controversy by giving Siegenthaler personally identifying information about the guy who added the false information in. So, this controversy is also an example of Nice Job Fixing It, Villain!
Such things were bound to happen from the very premise of the game. It's like spilling heaps of oiled sawdust all around the shop: one can always blame a smoker who walked by at night and didn't read the sign in big letters on the other side of the building, but dismissing any thoughts about fire safety made the result simply a matter of time.
During one campaign in the Global Guardians PBEM Universe, the "ape-liberation" terrorist group Prime 8 attempted to detonate a high-yield nuclear weapon in downtown Paris. The Global Guardians stopped the simian supervillains... but during the course of the battle the heroes managed to knock down the Eiffel Tower (which, in turn, destroyed several square blocks of the city during its collapse). Oops!
It's also shown in the prequel comics that the anti-intellectual insults Justice Joe flings at the Mad Scientist villain he's fighting are why Dr. Horrible decided to switch from admiring the heroes to becoming a villain in the first place.
Linkara's "Lord Vyce" story arc ended with this. Long story short, the Earth is being threatened by the feared intergalactic conqueror Lord Vyce, who claims he conquers worlds to "protect" them from being invaded by a much greater threat. Linkara and his nakama defeat Vyce, strip him of his weapons and leave him stranded on a desolate planet. At the episode's end, we see that the evil entity Vyce spoke of is very real—and now that Vyce is out of the picture, it's free to roam in our reality.
It's worse than that: Linkara has the entity's sacred tome in his possession, and he casually and routinely rattles off passages from it during his reviews. He didn't just leave our world vulnerable to attack from an Elder God—he might have unleashed it!
Suburban Knights: The Cloaks, the obstacles, and Jaffers are actively trying to stop the reviewers from finding the Gauntlet. Turns out they had a good reason to do so. Malachite was tracking Team 2's map, meaning that he wouldn't have found the gauntlet in the first place if the reviewers hadn't gone looking for it.
In Pay Me, Bug!, the protagonist has some security forces pinned in a stairwell; that is, until he mentions that he only has one pistol in a voice loud enough for them to hear him.
In the Whateley Universe, uber-mage Fey has stopped the Necromancer three times and defeated the supervillainess Hekate. Only just recently have we learned that every one of these battles has caused Fey to draw enough life energy from ley lines that she has caused ecological disasters each time. Oops.
During the Birthday Brawl, Bladedancer gets word from the Tao that the hostage situation to which she and Generator have been called will resolve itself without anyone getting hurt as long as nobody tries to go inside and intervene. Bladedancer and Generator are perfectly happy to just sit around and wait, but one of the local superheroes, a moron who doesn't respond to the police trying to flag him down, decides to charge right in and everything goes to hell.
In the Season 2 finale of Noob, Omega Zell tries to use a hacker-made item to quickly kill the enemys of Justice, the guild he dreams of joining. The problem is that the item works in a completely random way and all it ended up doing was earasing the avatar of Justice's top player.
In Ranged Combat, just as the RED Sniper Jarated the BLU Spy, his Heavy, Soldier and Scout teammates all pose as snipers, confusing and scaring off said BLU Spy. Then when the Sniper tried to get a clean kill off the running Spy, his focus got broken by the teammates trying to shoot the Spy with their short range weapons, allowing the Spy to run free. That really pissed the Sniper off.
In Subtlety, the BLU Spy is about to land a backstab on the RED Heavy... only for the BLU Scout to rush forward and start whacking the Heavy with a frying pan. The Heavy is not pleased, and neither was the Spy.
At the end of Ducktalez 3, Vegeta is defeated by being thrown into the sun, which explodes the sun and covers the world in eternal darkness. Nobody seems to mind though. Every Ducktalez since then takes place at night.