In Aquaman: Andromeda, in a story Tom Curry tells to his son, he reveals that after Atlanteans used the Darkworld's thought-shaping powers for their own benefit, it made the people's worry that Atlantis would sink manifest and actually happen.
At least two or three of his Rogues Gallery have been created this way as well, mainly by accidentally causing their downfall (at least one of The Joker's Multiple-Choice Past stories have him being scared by Batman and then either falling or jumping into the chemicals that result in his current look, and in some adaptations of The Riddler's backstory, it's implied he once worked as a game programmer before Bruce Wayne fired him), both in the comics as well as in various adaptations of the comics. Nice job breaking it, Dark Knight.
The events of Death of the Family are this: Bruce Wayne, early in his career, confronted the Joker after he's first incarcerated and makes the mistake of giving a hint of who he is to the Clown Prince. Cue a few years later in-series, and the Joker decides to destroy Batman's family and bring everything back to square one. Oy, Bats...!
Being Crazy-Prepared, Batman has a marked tendency to create draconian plans in case he ever needs to, say, destroy the Justice League or trigger a massive gang war. Unfortunately, he is also terrible about securing said plans. Thus, it is basically inevitable that someone will end up stealing these plans and using them against his allies. The first time this happened, Ra's Al Ghul nearly killed the Justice League, and he turned out to be a trendsetter.
Then, there's War Games. Stephanie Brown, pissed off at being used by Bruce, decides to use one of Bats' contingency plans to gather up all of the gangs and put them all under the control of mobster Matches Malone. However, she had no idea that Malone was actually an alias of Batman's, and when he didn't turn up at the meeting, everything went to hell. End result? All of the gangs killing themselves, leading to a massive power vacuum that ends up with Black Mask in charge.
When a minor villain named Cluemaster (a Riddler expy) was captured and sent to prison, it did cure him... of his obsession to leave clues.
Everyone who Batman met in the prelude to Dark Nights: Metal as he investigated a trail of mysterious super-heavy metals told him his research was a godawful idea, that it would only bring ruin and devastation, plainly incredulous the Dark Knight would be so utterly obsessed as to actually follow a trail to damnation. He just pushed onward to find the root of the mystery. Cue him breaking the seal on the Dark Multiverse and unleashing the demon Barbatos and his Dark Knight followers.
The Attack of the Annihilator: When the Big Bad blasts Supergirl out of a lab building and Batgirl points out his little show of force has started a fire, the Annihilator notices the flames and comes up with the idea to burn the whole building and its occupants to ashes.
Batman: The Imposter: This is what kicks off the central plot. Sometime prior to the events of the mini, Batman and Captain Gordon exposed a couple of judges with Mob links. This in turn led to all the convictions handed down by those judges being overturned and dozens of violent criminals being released. The imposter Batman is a disgruntled cop who blames Batman for this and tries to "set things right" by killing the released criminals and framing the vigilante for it.
The vigilante Ghost-Maker brags he can do everything Batman can even better, he just doesn't waste time with things like taking crooks in alive. He brags in a fight on how, in one night in Gotham, he took down a serial killer, a ring of corrupt judges and a secret arms deal, boasting on how "you didn't know about any of those." Batman fires back not only did he know but he was trailing the serial killer to find evidence on where he disposed of his past victims, all those judges were about to be indicted on a RICO case and he bugged the gun shipment to find the source. Now, thanks to Ghost-Maker, the killer will never give up the locations of the other victims to give the families peace, the actual mob bosses of the corrupt judges get off scot-free and there's no tracing who's shipping the guns. Ghost-Maker tries to shrug it off but it's clear he's shaken realizing his faster methods really aren't better.
In the Batman Vampire trilogy, this is how the third book, Crimson Mist comes about: At the end of Bloodstorm, Batman asks Alfred and Gordon to shut him down after he kills the Joker and drinks his blood. They stake his heart, but don’t remove his head, thus he suffers from And I Must Scream until Alfred removes the stake, turning him into a blood-hungry monster.
In Booster Gold vol. 2, when he goes back in time to save his friend Ted Kord, the second Blue Beetle. He succeeds, but since Ted's death is the nudge that brought the other heroes into action barely on time for the events of Infinite Crisis, his salvation results in the heroes failing to act on time, leaving the world in ruins and under Max Lord's domination.
In Convergence: Superman #1, the pre-Flashpoint Superman's attempts to reason with Captain Thunder and the Flashpoint versions of Cyborg and Abin Sur are foiled when the pre-Flashpoint Jimmy Olsen, wanting to help Superman, attacks the Flashpoint heroes with an armed aircraft.
In Convergence #7, Parallax kills Deimos but this let loose of all the powers Deimos had drained from the time travellers to BREAK all of reality apart.
Barry Allen decides that he doesn't want his mom to be dead anymore. So, he goes and chases Professor Zoom and stops him from killing his mom. End result? Flashpoint (and an immortal Zoom). Oops.
He did this literally, on a smaller scale, in one issue of his original run. The Mirror Master falls in love with a woman trapped in a mirror, and tries to rescue her by tricking the Flash into taking her place. Barry realizes he's being sucked into the mirror—and shatters it, which traps her forever. Oops.
Ah, the Guardians of the Universe. Living proof that age does not necessarily equal wisdom, as it seems that in one way or another, pretty much every single one of their decisions backfires spectacularly. Highlights of their past decisions coming back to bite them in the ass include the roboticManhunters, rogue Guardian Krona, rival corps such as the Red Lanterns and the Sinestro corps, and, last but not least, the events of Emerald Twilight. And that was beforethey went off the deep end. It is not an exaggeration to say that most of the conflict from the GL books stems in some way from the Guardians. No matter what decision they make, action or non-action, it always ends up being the wrong one.
When the Corps executed Sinestro in Green Lantern Corps vol. 1 #222, Sinestro transferred his soul to the Central Power Battery and imploded it from within (rendering almost all of the power rings powerless, with the exceptions of Hal, Guy and Ch'p), and that's when he discovered the yellow impurity (if we go by current continuity, that yellow impurity is Parallax).
Guy Gardner, in Green Lantern Corps #16, "Falling Star", botches a sting operation that was 2 years in planning by the Feds and local police, when he pulls a Leeroy Jenkins and crashes the setup, sending all their hard work down the crapper and getting himself incarcerated in the process.
Hellblazer: It happens all the time; it's a fact of the protagonist's life that he never has any permanent, unequivocal victories.
In Hellblazer: Rise and Fall, John had summoned a lesser demon when he was younger, the demon possessing a banker's son and, after gaining strength in the streets of London, took Lucifer's wings.
Heroes in Crisis focused on Sanctuary, a safe haven Batman, Superman, and Wonder Woman created so superheroes could have a place to receive therapy. While the idea was a nice gesture, it was awfully half-assed. The place had no doctors or therapists, they delegated all the work to a computer programmed with their "best qualities" and all said computer did was make the patients relive their respective traumatic ordeals through virtual reality chambers while mocking them about it, and the patients were largely kept isolated from one another, which was making the patients worse. In fact, Wally was so thoroughly broken he started thinking Sanctuary was a set-up by supervillains to torture heroes, hacked the computer and ended up experiencing everyone's trauma at once until he had a nervous breakdown and unwillingly unleashed a burst of energy that killed everyone around him. Later, it was retconned so that the surge wasn't actually caused by Wally's depression, but the Speed Force trying to kick Savitar out of itself and the cover-up was due to Wally's mind being screwed with by Eobard Thawne. Which still doesn't change the fact that Wally and a lot of other people spent weeks being mentally and emotionally tortured thanks to the Trinity's utter half-assing.
In Jenny Sparks: The Secret History of The Authority, we find out that a thirteen-year-old Jenny Sparks (a blue-eyed blonde girl) convinced a friend in Vienna that he was wasting his life making paintings that didn't sell and suggested that he'd find another profession.
Jenny Sparks: There must be something you can do. You're patriotic, well-read and an excellent communicator. Have you ever considered a career in local government? Do we even have to say it?: Politics? Actually, that might not be such a bad idea.
Joker's Last Laugh would not have happened if a doctor hadn't decided that lying to the Joker and tell him he has cancer to screw with him was a good idea.
Almost and sort of happened in the Rock of Ages storyline. As Superman and the other mainstringers of the JLA go after Lex Luthor, who has acquired the Philosopher's Stone and formed his own Injustice Gang, it is revealed to Green Lantern, Flash, and Aquaman that the JLA will eventually defeat Luthor and the Gang, and Superman will destroy the powerful Stone… which will somehow cause Darkseid to conquer the Earth. They even get a firsthand experience of that dark (pun not intended) future. This future is averted when they get back barely in time to give Martian Manhunter a warning for him to stop Superman from destroying the Philosopher's Stone.
Definitely happened in the Midsummer's Nightmare storyline (which caused this JLA incarnation to form in the first place): after foiling the Big Bad's plan, he explains he only did it to prepare humanity for a worse threat Mageddon that was still to come.
In their battle with the invincible supervillain the General, Batman tries to use hypnosis to defeat the villain. He does a good job until Superman comes bursting through the wall. Batman even yelled at Supes for the screw-up.
Justice League: The Rise of Arsenal became less about Roy Harper's downward spiral in anti-heroism following the death of his daughter Lian and his dismemberment by Prometheus, and more about what happens when you neglect a friend when he needs you most. This was due to the astonishingly half-assed approach his friends and family took when trying to help him.
In Part 4 of Night of the Monster Men, Gotham Girl kills a monster by ripping its arms off. However, this drenches her and Nightwing in its blood and causes them to mutate into monsters themselves.
Supergirl did this twice in Red Daughter of Krypton. In Red Lanterns #31, Supergirl tries help a Red Lantern get her mind back by taking a tank of lake blood and ripping it open over the city that Sheko -the above-mentioned Red Lantern- is in. Unfortunately, Atrocitus is present, and he takes control of the blood rain, making it into a tornado. So Supergirl tries to fix the mess. Unfortunately her way to fix the blood storm is to ignite it with heat vision. The result conflagration sets the city on fire.
Supergirl: I thought I was doing the right thing. I was "Supergirl", right? I always do the right thing. The man I took back, his name was Reactron. He was the end of my people. Because of me, they're gone. Kal said even super-people make mistakes.
Godship remained orbiting Bizarro World for days until Bizarro decided to kick it out. Bizarro thinks he might have made it mad because then it sent a swarm of monsters after him.
War World: In order to save his friends from villain Mongul, Superman fights Martian Manhunter and retrieves a special Key from a crypt. Later he refuses to hand over the device, but Mongul manages to get his hands on the Crystal Key and start Warworld, a satellite super-weapon.
In Who Took the Super out of Superman?, the Man of Steel breaks a solar storm apart, unaware that it was disrupting the functioning of the super-suit of villain Solarman. His suit working fine, Solarman goes on a crime spree.
In Superman: Brainiac, Superman leaves Earth to look for Brainiac. However, Brainiac captures him and learns the coordinates of Earth and the existence of Supergirl from him.
In Superman: Doomed, Sam Lane authorizes Metallo to attack SuperDoom with Kryptonite bombs. The ensuing blast kills Metallo and covers the entire continent with a Kryptonite cloud, but SuperDoom survives and the Kryptonite only makes his condition worse.
Superman had two such events that occurred in Action Comics #544: Luthor Unleashed!:
A super-weapon that eats stars created by Brainiac before Superman reprogrammed him for good proves too powerful for Superman (it can analyze attackers and uses energy from red suns it's eaten against him) so Superman seeks Brainiac out but he can't remember information about it as that's in his 'evil' partition. Superman ignores Brainiac's rejection of being made evil again and uses his superspeed to forcibly return Brainiac to evil knowing he can't reverse it again. Brainiac quickly uses it to try and kill Superman only for Superman to defeat him and imprison him within the planet it's created inside. His attempt to escape results in his transformation into the far more dangerous metallic steel Brainiac with the Skull spaceship.
After defeating Lex Luthor's latest scheme prior to the story start Superman leaves the critically ill Luthor there and flies off to deal with something else while noting Lex likely will pass out before he's out of sight. Lex pull himself to safety just before his burning ship explodes which would have killed him. Rescued by one of his advanced robots and sent to Lexor to recover he creates (later retconned into discovering) the upgraded battlesuit that's become associated with him in media from that point on.
In a story that was later retconned, Superman tried to combat the Spellbinder's crime spree by hypnotizing the population of Metropolis (with their consent) to resist Spellbinder's own hypnosis. Of course, when Superman next confronts Spellbinder, he finds he's taken the Boring, but Practical route of just shooting people in the way of his crimes, which he wouldn't have chosen to do had he managed to hypnotize them as usual.
In the "Five Years Later" era of the Legion of Super-Heroes, Cosmic Boy's (or, rather, the Time Trapper's) attempts to protect the Legion using the abilities learned from the Infinite Library in "End of an Era" only make the already-bad situation worse.
In The Great Darkness Saga, Mon-El tries to engage the Master of Darkness in the Sorcerers' World. Not only does Mon-El fail to take him down, but also he accidentally reveals the existence of a planet worth of Kryptonian-like beings.
During the events that'd lead to Ferro Lad's Heroic Sacrifice, the Legion of Super-Heroes turned to a group of five super villains for help in dealing with the Sun-Eater — the Fatal Five, who'd go on to be persistent pains in the Legion's asses.
In Escape from the Phantom Zone, one jailer gives the sorceress Selena one stale, moldy loaf in punishment for her latest offense. Though, the mould growing throughout the bread gives Selena a tool to bypass her cell's anti-magic protection, and she is able to cast a spell to get rid of her guards and blow her cell up.
The Phantom Zone shows that Lara Lor-Van foiled the Phantom Zoners' attempt to telepathically influence her husband Jor-El into getting them out of their dimensional prison. Thanks to her well-meaning intervention, dozens of Kryptonian criminals will survive Krypton's destruction and plague her son, niece and Earth people for years to come.
Day of the Dollmaker: Supergirl blasts one killer doll away from Cat Grant, but by doing so she accidentally destroys some evidence needed to find a child kidnapper. Dollmaker's killer doll mocks her by it before coming apart.
Dollmaker:"And here Ms. Grant thought you would be the one to get her out of this tree, and you've just melted some key evidence. How sad."
In Superman/Supergirl: Maelstrom, Kal and Kara travel to an alien planet. When they find out that several alien monsters are messing up with their ship, Supergirl throws one rock to scare them off. Though, one of them retaliates by shooting a venomous dart which hits Superman in the chest.
The Dominator War: Booster Gold unwittingly causes the war by stealing a Dominator weapon and boasting about saving fifty-two worlds before disappearing back into the time-stream. The Dominators never found out his identity or intentions, but they were incensed at the humans breaking the peace treaty, and they misinterpreted his words as Earth having allied fifty-two worlds against them covertly.
In Swordquest: Waterworld, Captain Frost kills a snow-whale to prevent them from siding with the local mer-people in a possible war, but that's the very atrocity that prompts them to immediately declare war.
During the one-year Time Skip (long story), Raven spent several months working on bringing her old friend, Joseph Wilson, back to life. She succeeded, and what was the first big thing Joey did after returning from the grave? Tried to murder the Titans.
Another example is when Damian joins the team. The Titans are fighting a rampaging teenage psychic. Raven is able to calm him down. Then the Boy Wonder kicks him, pissing him off even more.
.Jenny Sparks: There must be something you can do. You're patriotic, well-read and an excellent communicator. Have you ever considered a career in local government?