Happens on a major scale in the Marvel crossover event Age of Ultron, when Wolverine's jumps through time tear open the fabric of space and time, creating a multiverse crisis.
In an early Avengers issue, the team has come to a military base to locate the Cosmic Cube, an all-powerful wish-granting machine. They find Prince Namor the Sub-Mariner trashing the place for unrelated reasons. During the fight, Hercules tells Namor they'll never let him get the Cosmic Cube. Namor promptly escapes, leaving Hank Pym fuming — he's guessed (correctly) that Namor had never heard of the thing until Herc told him. Naturally, Subby finds the Cube and comes back to mop the floor with them.
Avengers vs. X-Men: The Avengers manage to disrupt the Phoenix Force before it can possess Hope... only to split it into five units, which then possess Cyclops, Namor, Emma Frost, Colossus (who was already possessed by the Juggernaut!) and Magik. The Phoenix-possessed X-Men then proceed to use their new power for the greater benefit of all mankind, solving world hunger, making deserts bloom, bringing free clean energy to every corner of the globe and even bringing about an end to war... then the Avengers decide to attack them again. By this time, though, it was established that the Phoenix Force was making the Phoenix 5 unstable, leading to them doing things like giving whales crab legs so that they could walk on land or deciding that any negatives they faced could simply be fixed with more Phoenix Force.
During Civil War II, Hawkeye killed Bruce Banner. It is revealed that Bruce had asked Hawkeye to kill him if it looked like he would ever again become the Hulk, and had even given the archer a special arrow tip to do the deed with. As a result, the Hand was able to acquire Bruce's body and turn the Hulk into a brainwashed servant of theirs, and Jennifer Walters has another bit of trauma and anger to deal with. Meaning that she's becoming as savage as the Hulk was. Um...oops?
In Matt Fraction's 2011 The Defenders series, the heroes accidentally meddled with one of the Concordance Engines — mysterious artifacts that keep the 616 universe running as it should — in the very first arc. The rest of the series involved them learning how badly they'd messed everything up, and eventually Doctor Strange had to go back in time and retcon their mistake (and the whole series) out of existence.
Done on a universal scale by Reed Richards. Reed learned some time ago that Galactus' existence, however problematic, is necessary to the universe. He tried to get around the problem by turning Galactus into a star. In mainstream continuity, this still ends up releasing Abraxas. In Earth X, it frees up the Celestials to overrun the universe (because what Galactus was really eating was their young, which gestate in planetary cores — then hatch).
Done a lot in the Byrne Era. The only characters who don't mess up royally are Sue and Johnny. For example: Reed invents a portal to the Negative Zone. He then takes Sue, Johnny, and Ben to the Negative Zone for a long time without even considering the fact he didn't even program the portal to only recognize them, and not allow anyone else in. Oh, not only that Reed never once considers asking the Avengers to watch over Alicia and Franklin in the Baxter Building, leaving them completely and utterly defenseless in case of an attack. The result? Alicia and Franklin are nearly killed by Annihilus, half of the Baxter Building is destroyed, and Annihilus almost destroys New York yet again. And...no one calls out Reed that stupidity. Not even Sue!
Another point: Thing decides, against all logic, to stay on Battleworld. He returns months later, learning Alicia had moved on and fell for Johnny (which was mutual). Ben, we love you, but come on, you ABANDONED your blind girlfriend after she had been fucked up by Annihilus to stay on another planet due to your self-centered body issues. And you expected her notto move on? Granted, "Alicia" was really the Skrull Lyja, but even so...
Even more heartbreaking because Reed KNEW that the Thing was staying on Battleworld because he thought it was why he could transform but Reed knew that it was a mental block that Ben had that was responsible for him being stuck in Thing form. The mental block went away because Ben was convinced they'd never survive Battleworld and the reason for it no longer mattered. Reed chose to not tell Ben and leaves him behind instead rather than admit he knew the real reason for it, resulting in Ben months later killing his human side and returning to Earth. Only when he returns does Reed tell him the truth after it's far too late (and gets a blow that actually leaves Reed with a bruised face, something normally impossible).
The Incredible Hulk: General Ross has unwittingly and sometimes deliberately stopped Banner from curing himself of the Hulk many many times, not to mention acting as the catalyst for pissing off Banner and thus transforming him into the Hulk even more often. Ross' attempts to stop the Hulk only tend to make things even worse. Whether an incident falls under Nice Job Breaking It, Hero or Nice Job Fixing It, Villain depends on which side of the Face–Heel Revolving Door one considers Ross to be at the time.
Kid Loki is directly to blame for all the final conflict in his run of Journey into Mystery (Gillen). Actually, Kid Loki's entire run is a breathtaking example of this trope in action. Mostly powerless and mistrusted by nearly everyone, Loki's only recourse to solving the problems he encounters is to knowingly and willfully break other things. The final conflict is, essentially, everything he's done catching up to him.
The Mighty Thor: In-universe, almost everyone considers Thor bringing back Loki (after he died in Siege) to be this. Loki was, however, brought back as a kid without any of his former emotional baggage (this was discovered to be one last shot at redemption/something like that by the original Loki). The trope's been subverted because so far the kid has one goal in mind: save Thor from the Serpent (and he if saves Earth too, then that's great!).
Plus, Thor insists that the real Nice Job Breaking It, Hero was how all of Asgard treated Loki as a villain because that's how it was written by the Norns, and therefore he became the villain they scorned him as. The main argument Thor has for keeping Loki alive is that with the Ragnarok cycle broken, even Loki has a chance to be good, and not have his fate predetermined.
Odin seems to be setting himself up for one, with the whole "raze earth to the ground to kill one enemy" thing. That won't come back and bite you in the butt ever. After all, the citizens ofMarvel comics are so forgiving.
They're only unforgiving if you're a good guy. Bad guys says he's reformed? Let's put him in charge of S.H.I.E.L.D.! Nice job breaking it, Muggles.
In one of the tie-ins to Original Sin, it's revealed that during World War II, The Invaders had a chance to defeat Imperial Japan without dropping the atomic bombs, but chose not to go through with it. The explanation given is that Golden Girl and the Kid Commandos purposefully sabotaged the plan, as it would've endangered the lives of a bunch of native islanders living near the Japanese coast. The plan's failure is what led to President Harry Truman's decision to bomb Hiroshima and Nagasaki, resulting in far more civilian deaths than would have occurred had Golden Girl not interfered. Radiance, Golden Girl's granddaughter, understandably goes berserk when she learns this.
The Skrull prince Xavin put a great deal of effort into guilt-tripping Karolina Dean into leaving the Runaways and becoming his/her bride in hopes of ending a war between the Skrulls and the Majesdanians that had been sparked by Karolina's evil parents. But their betrothal actually ended up re-igniting the war and making things worse.
Nick Fury decided to go after Latverian terrorists in the Secret War crossover. But he didn't get the job done all the way, and the entire thing ended up biting him in the ass, with Luke Cage and Jessica Jones in particular almost getting killed, and Nick on the run for his life from the very organization he had led for years.
Also happens in Marvel's Crisis CrossoverSiege. The Avengers assemble in Asgard to defeat Norman Osborn, reuniting the 'Big Three' of Marvel; that is, Captain America, Iron Man and Thor. Osborn is defeated, but not before having The Sentry destroy Asgard. It then turns out that Osborn was the only one who could control the Void, the Sentry's evil side, who, as the president was informed, "has no limit to his powerset". The Void is then shown preparing to kill them all.
Sleepwalker has just about defeated the Ax-Crazy Psyko and halted his rampage across New York. It's then that he sees a man who's possessed by a demon and uses his warp beams on the man to expel the demon, which provokes a watching Spectra to attack him. While Sleepwalker defends himself from Spectra, Psyko seizes the opportunity to escape and continue running amuck through New York. Fortunately, Spectra later fixes her mistake when she helps Sleepwalker bring Psyko to justice once and for all.
He actively attacks The Avengers when they worry about him, then put him on probation when they can't really find anything wrong and suggest he's just taking things a tad too far.
After obtaining his own mercenary force and obtaining the Raft to turn into Spider-Island, he invades Shadowland and apparently kills Wilson Fisk. Not only is Fisk not dead, the Green Goblin swoops in and gathers up what remains of Fisk's forces to become the Goblin Kingpin of Crime.
When he's searching for the new Hobgoblin, he goes so far as to reveal the man's identity to the entirety of New York. With nowhere left to run, the man finds himself running into the loving arms of, you guessed it, the Green Goblin.
His ultimate breaking? Erasing Peter Parker's memories from his mind. In his attempt to prove that he's better than Parker in every way, he eradicates what seemingly is what's left of Peter's memories. End result? When Horizon Labs is on the verge of being destroyed and another hero, Spider-Man 2099 attempts to save the day, SpOck promptly knocks him out, then attempts to save the day himself. Because he erased Peter's memories, he's trying desperately to find one of Peter's memories before he's blown up temporarily and, thanks to a bit of a time glitch, loses about nine hours of life. Thanks to this, Horizon Labs is gone, he's lost his job, Spidey 2099's stuck in the past... oh, and Peter's coming back.
Not that Parker himself has done much better. His 'solution' to the Goblin Nation mess was to cure Norman Osborn's insanity. While this might seem like a good idea, it's obvious that without Green Goblin holding him back, Normie is going to be a far more cunning and insidious super-villain than the cackling lunatic he used to be.
In Spider-Man: Life Story, Claire Parker encouraging her father to go to New York and return as Spider-Man while talking him out of his plan to move the family away ASAP, ultimately left them undefended from Morlun's, leading to her brother's near-death.
In Spider-Man: Blue, Peter goes to seek help from Curt Conners, in order to help defeat the Rhino. This exposes the good doctor to certain chemicals that trigger his transformation into the Lizard.
The Ultimates (2015): As part of their team mission, the Ultimates try to travel beyond the edge of all existence, to try and "fix" the broken timeline. It doesn't work, partly because other parties persuade them to go home. But the dimensional hole they punch draws the spirit of Thanos back to the world of the living, which causes the events of Civil War II.
War of Kings: After the events of Secret Invasion, the Inhumans decided they had taken enough being pushed around, and go after the Skrulls. Their first and only strike, using Black Bolt's voice, utterly destroys the ragged Skrull fleet... and punches a hole in reality, awakening the long-dormant Fraternity of Raptors (a Magitek Shi'ar cult of assassins). It also provokes Vulcan, who takes it as an excuse to invade Kree space to try and kill them, kickstarting the whole war. Later on during the war, said Fraternity assassinates Lilandra, just as she was trying to depose Vulcan and regain control of the Shi'ar, to try and end the war.
Amazingly, it does not get better. At the conclusion, Black Bolt and Vulcan get into a fight which tears open a massive Negative Space Wedgie named The Fault. Adam Warlock, of the Guardians of the Galaxy, goes to fix it, but his methods not only cause the return of The Magus, it begins violently overriding every possible future with one ruled by the Universal Church of Truth. The Guardians manage to prevent that, but the Magus uses the Fault to summon the Many-Angled Ones to take over the universe. That eventually results in Star-Lord and Richard Rider having to sacrifice themselves. All because of Black Bolt.
In The Dark Phoenix Saga, Beast attempts to take Lilandra's offer to leave the trial of Phoenix because he was not technically an X-Man, planning to come back with all of his fellow Avengers to help, only for Angel to declare that there was no way he and Beast would abandon their friends in their time of need.
The Brood Saga: Logan decides to keep the information about his friends being infected until they have escaped the Broods’ advances and everyone has become sufficiently freaked out about whatever is going on between their bodies such as Kitty’s resistance to cosmic radiation and Storm’s sudden illness. Had he told them earlier Storm may not have had her Freak Out and left on a scout ship and Carol wouldn’t have left on her Roaring Rampage of Revenge (she had just turned into Binary) and punched a hole through the ship’s wall, nearly causing everyone on board to be sucked into space.
Cable managed to kill En Sabah Nur in the 12th century, before he could become Apocalypse. Later, he learns that the blood he spilled in that fight mingled with Nur's and resurrected him, made him techno-organic, and gave him the ability to interface with Celestial technology, effectively creating Apocalypse in the first place.
First there's the titular villain's very existence: After Magneto ripped out the adamantium from Wolverine, Xavier lashed out and used his powers to mindwipe Magneto — resulting in a piece of Magneto's dark side attaching itself to Xavier's, festering and building with each additional failure (a mutant kid being murdered by a mob near the X-Mansion, failing to rehabilitate Sabretooth, Creed nearly killing Psylocke during his breakout) until it became the titular split personality of Xavier's.
Nate Grey forcefully dragging Xavier's out of the astral plane and into the physical world gave Onslaught the means to form a psychic body for himself and move independently of Xavier.
Until a numbers of heroes, including The Mighty Thor once combat Onslaught, doing damage and allowing Thor to free Xavier — except not only did this not end Onslaught's threat, Xavier was actually holding Onslaught back, resulting in a now-unrestrained Onslaught.
The Hulk destroyed Onslaught's body — resulting in his becoming a being of Pure Energy, which is what he wanted — though this was also a case of Nice Job Fixing It, Villain as he was finally able to be defeated in that form.
