During the development of Atari's Superman pinball, Steve Ritchie and Eugene Jarvis figured out how to use a guitar echo chamber to make a continuous background sound that intensified with the game action. For some reason, Atari management nixed the idea; Ritchie ended up using it on his next pinball, the top-selling Flash from Williams Electronics.
In Yu Gi Oh East Academy, we have a subtle example from Marcus during his Tag Duel with Denero. While his strategy is solid, it unfortunately has the unforeseen consequence of being indirectly responsible for Denero merging his mind with the Meteor and becoming more aggressive and unstable as a result.
DS unknowingly made a few comments that inspired the Impossible Thief Emolga to steal Tagg's cynical side. As a result, Nihilist!Tagg was unleashed, and some of the trainers had to fight for their lives while DS went off to find the Emolga and get Tagg's cynical side back so he could be returned to normal.
Tagg ends up starting the Keystone arc by taking Annoski's Keystone to the spot it needs to be for him to revive.
During PMD-B Tagg's group allowing the last two Super Mutants to get away doomed Necropolis by having the Master send his army to destroy the place in reprisal.
The whole goal of the heroes in BIONICLE is to awaken the sleeping Great Spirit Mata Nui. Unfortunately, Makuta (who put Mata Nui to sleep in the first place) plays them all for Unwitting Pawns: he allows the heroes to succeed and during a window of opportunity in the revival commits Grand Theft Me, taking control of the body of a Physical God and therefore also the world's very laws of nature. Nice Job Waking It, Heroes.
In extreme cases, there's the Permanent Red Link Club, in which the tropes are so misused, become a magnet for racial slurs and personal attacks, and the like that not only the page is locked, the page (and in some occasions, the entire trope) gets deleted, never to be used again. Forever.
And in less extreme but still unfortunate cases, Real Life examples can be cut and prohibited from a page if things get controversial enough. On that note, there's also the Example Sectionectomy, which examples are either cut entirely or relegated to a separate area such as Darth Wiki or the Discussion tab if things get nasty.
And if the examples had previously been divided into multiple pages, then the deleted Real Life examples won't even appear in the page history for you to browse.
Troper Tales existing in the first place. Troper Tales was only created to keep tropers from writing their own tales on the main wiki. Troper Tales ruined the reputation of TV Tropes and made the website a laughingstock of half the Internet. It was also known for attracting people who wrote stories that sounded creepy, filled with bile, psychotic, racist, sexist and ego-stroking. The admins could have either warned the tropers or banned them for writing personal tales instead of creating troper tales, since Troper Tales only reinforced the habit.
TV Tropes used to have a "strike format", but it was eventually disabled as people were using it simply to sneak in Take Thats and such. Texts that were previously striked are now hidden texts. The strike format however is still usable in the forums though.
Earlier there were "super secret spoilers", which was the equivalent of making the text white. This was also removed in part due to people actually using it for relevant information that reader couldn't see without highlighting the whole page.