In Sluggy Freelance, when Torg exorcises the demon K'Z'K out of Gwynn, he sets K'Z'K free upon the world. Subverted in that this was actually intentional: they needed the Demon out of Gwynn so that they could use their plan on it directly and not harm her. However...
Done again almost immediately afterwards, when Riff's attempt to freeze the demon in time actually sends it back in time, creating all sorts of havoc during the middle ages.
In The Order of the Stick, after defeating Xykon and scattering his forces, Spoony Bard Elan activates a self-destruct rune that blows up the entire dungeon because he wanted his dramatic Outrun the Fireball scene. Turns out that the self-destruct took out the magical gate that was sealing a world-destroying abomination whose destruction brings the world one step closer to destruction. The only consolation of this massive act of stupidity was the Gate couldn't be recaptured by the Lich and his crony after he reformed (because the Order wouldn't have any idea that they needed to secure it). They ultimately decide that in hindsight, this was the necessary thing to do, even if they didn't know it at the time.
In an example later in the comic, Bunny-Ears Lawyer Celia manages to make a settlement with the local Thieves' Guild. While this settlement fixes a lot of their problems, part of the agreement was that Haley (who betrayed the Guild in the past) donates 50% of her loot to the Guild as apology. Since all this loot is part of her "get her father out of jail" fund, she is... upset, to say the least.
Haley doesn't even have the loot anymore. To pay off the Guild at all she'll need to steal twice that much over again, giving 50% of the new thefts to the Guild outright and paying off the balance with the other 50%; just to end up back at zero as regards getting her father out of jail.
Haley gets out of this by killing Crystal and leaving when they meet up with the rest of the group.
In an example earlier then the above one, Miko Miyazaki chooses precisely the wrong moment to destroy the Gate of Azure City - if she had been stalled for even a few more rounds, Xykon and Redclock would be dead and the goblin army wouldn't have had its highly competent leader and incredibly powerful Sorcerer to consolidate their conquest of Azure City.
Girard, one of the creators of the Gates, was paranoid that his former associate and fellow Gate-maker Soon would break their vow and try to interfere with the Gates. So he gave Soon and everyone else the wrong coordinates for his gate, booby-trapped the decoy area, and gave the real location to the one person he trusted, Serini. Thing is, Soon never broke his word, being a Paladin. When the decoy area is approached years later by the Order of the Stick to try and defend it from Xykon, they're almost killed by Girard's paranoia and have no idea where the real Gate is. And guess who has his bony hands on Serini's diary?
In Start of Darkness...
Lirian: Even if you locate them, my friends will stop you from conquering the other four Gates.
Vaarsuvius, while drunk on the power of three epic evil spellcasters, defeats a black dragon that was menacing its children. He/she casts the genocidal spell Familicide on the dragon, which exterminates the dragon's entire bloodline, and any creature related to that bloodline. Later it's revealed that Girard Draketooth, the epic-level illusionist that is charged with protecting one of the all-important Gates, was the grandson of a relative of said dragon. Thus his entire clan was wiped out by the spell, leaving the Gate defenseless.
In the first chapter of Gunnerkrigg Court, Antimony helps a lost Shadow-Man return to his forest home, by assembling a Robot to escort him there (since the rules prohibited Annie from going herself). She also tells Robot that he only has to return to the Court afterwards if he wants to, so he decides to go exploring the woods. Several chapters later, Robot returns, possessed by another, violent and malicious shadow-creature, and the process of stopping the shadow results in Robot getting impaled on a BFS and deactivated. A few chapters later, Annie finds out that the people of the forest have not been on good terms with the Court for the past decade, and that they hate technology on principle. Nice job completely screwing over your friend and causing a diplomatic crisis, hero.
8-Bit Theater has a nice scene where Muffin Dragoon's pet parrot (dragon) reveals to the light warriors that Bahamut, who they had previously awakened, would only awaken when the world is about to be destroyed. Only Red Mage seems to care, though in retrospect any acts of "good" the Light Warriors do usually makes everything worse for someone else.
During the "Sin City" (no, not that one) arc of Dominic Deegan, Dominic reveals to The Infernomancer that the demon lord he was supposedly bound to serve didn't have control over him, meaning he didn't have to follow any orders. The Infernomancer's response? "Now I get to kill you the way I've always wanted to — slowly!"
Not to mention the "War In Hell" arc, where Dominic helps out Karnak the whole time only to realize he probably shouldn't have been helping Karnak this whole time.
In his defense, Karnak's death would have also killed Szark Sturtz, since he and Karnak will linked by a wound Karnak had inflicted on Szark when the latter was a child. You really can't blame Dominic for trying to keep his best friend alive. Plus, as pointed out by Dejah, there was really no way for the war to end positively for humanity.
And then there's Klo Tark, who started a prison break to (rather circuitously) save Dominic's life.
In Starslip, the crew (mainly Quine, though Vanderbeam initiated it) have done a Nice Job Ruining The Quel's Utopia.
And again with the Anthelerix. Both cases were such colossal screwups that Vanderbeam has since repeatedly suggested that Quine would do a better job of doing his job if he were to just sit quietly on the Paradigm someplace where no one has to look at him.
That comment is more due to Vanderbeam's irrational hatred of Quine. In the Anthelerix's case, the responsibility arguably rests with Admiral Huff. You'd think that the Paradigm being teleported back to Earth was a sign that maybe the Anthelerix didn't want anyone disturbing them for the time being, but noooo...
The party of Darths & Droids pretty much does this all the time, one of the most obvious being completely ruining Darth Maul's attempt to retrieve the Lost Orb. However, if the course of the strip is in accordance with the movies sufficiently, then they also inadvertently created Darth Vader and ensured the destruction of the Jedi...to win a pod race. But in their defense, they did win.
Don't forget: they only got into that pod race to raise money for weapons they never used anyway.
The FreakAngels had wanted to cause a huge but non-threatening destructive gesture as a means of putting the army off the notion of continuing to chase them (or at least distracting them for a while. Instead, their severe underestimation of just how powerful they are caused them to inadvertantly cause destructive shockwaves which ended civilisation.
In Homestuck Jade sends her friend John a birthday present. Using her precognitive abilities, she sends John a weapon to fight Jack Noir. Unfortunately, the Noir intercepts the gift and ends up using it to defeat the black queen and take her power. Jack then uses this power to singlehandedly obliterate both the black AND white armies and destroy the entire planet of Prospit, which ends up also killing Jade's dream self. Nice job.
In Act 5, we finally find out why the Trolls think the kids fucked up the game so badly. It's actually their own fault, as Vriska made John fall asleep, forcing Bec to prototype Jade's kernelsprite with himself, and granting Jack Noir near-omnipotence.
Retroactively. Bec Noir already existed in their universe, so whether or not Vriska did anything, the Kid's Session would still cause his existence. She just wants to kill Jack to prove her worth to the rest of the group.
Causality (or the lack thereof) doesn't seem to work that way. He existed in their universe as a result of Vriska's actions, which she performed more or less for the purpose of closing the causal loop — or rather, being the one to close the causal loop. Becsprite's creation depended on her own thought processes and ambitions. Though the loop itself seems to have had its own cause — see below.
In trying to do so, she leads Jack right back to where the others are. Oops!!!!!!!!
Then there's Karkat's big screw-up, which more or less caused everything that ever went wrong. He was in such a hurry to beat the game that he decided that the final frog needed to fix Bilious Slick's genetic sequence was unnecessary. Turns out that code was the only thing preventing the frog from getting a massive tumor, meaning he essentially gave the kids' universe cancer.
A recent Exterminatus Now comic had Yuri smash a panel that she thought was the power source for the daemon portal. Turns out, it may have been the control panel, given that its destruction released the daemons.
In Penny and Aggie, when Stan confronts the sociopathic Cyndi about her attempt to deceive his best friend Jack, and other classmates, into thinking she wanted to sleep with them, he taunts her for not thinking big enough, so as to imply she's lost her touch and shake her confidence. Instead, she says "You're right. You're so right," and giggles ominously. Stan himself admits in the next strip that he made things worse.
Congrats, Big Ears! Your Critical Failure at healing Complains' fractured arm has lead directly to Chief dying a slow, agonizing death.
In El Goonish Shive, Abraham and his great idea to make the Dewitchery Diamond. What he needed was to remove or suppress the lycanthropy of one guy. What he did is create a Booby Trap for unaware shapeshifters and users of cosmetic magic, with side effects that in turn suffer several other side effects in such a way that whatever problem caused its activation spreads. And it's nigh indestructible, so all this fun never ends.
It was Abraham. Others mostly settle on locking damn thing away.
Lets not forget the fact that good ole' Abe thinks it might be intelligent!
In Tales of the Questor Quentyn is sent on a quest to slay a dragon. He actually succeeds, but only after that success does he learn two critical facts:
There were two dragons, not one.
The one true Berserk Button for dragons is finding the body of a dead dragon.
The direct consequence of this is that the second dragon runs amok and lays waste to the Duchy Quentyn was trying to save. There are also hints that more long-term consequences await Quentyn in the form of a Corrupt Church whose attention was grabbed by this incident.
During the 1999 arc of Asperchu, Jivin stops past Bionic from committing suicide over Ian's rejecting of him. Considering the things Bionic would do in the present, it might have been better for everyone to let him die.
