Chosen To Destroy, written as a Take That at Buffy the Vampire Slayer and Angel, which has the First Evil show up after the Season 7 Buffy finale, basically to gloat over how it's going to open all the world's Hellmouths and kill all the Slayers in the world, and to rub it in that it's all Buffy's fault - while some of it was the First's manipulations, it makes it very clear that the main reason it's going to win now is because of Buffy's ego and stupidity (and Angel's to a lesser extent).
In Kage, the Guardians are quick to attack Jade when she arrives in Meridian, and that, combined with Elyon loosing control and nearly killing her, is a major part of the reason Jade ends up with the Knights.
Underestimates the Karate Club guys and gets in a position where she has to use a chi burst to defeat them in public, while Gauron is spying on Kaname nearby.
Naiki's fear of flying combined with a terrorist takeover of the plane she's on causes her to go on a fear-crazed berserk as soon as the plane lands, which leaves her captured and used as a hostage to insure Deimosu's surrender.
Goes back to help Kurz's fight against the Venom Chodarl, splitting the escape party and causing Eija, Kaname, Deimosu and Sousuke to hesitate long enough figuring out where she went for the Musk to attack and force Eija, Kaname and Sousuke to miss the escape.
Tries and fails to rescue and protect Tessa from the Behemoth terrorists.
Uses a black magic spell that causes her to touch Tessa's soul, starting the mind merge process and also indebting her to a Demon that makes Mara queasy. Twice.
In backstory, Naiki's intense fear of flying is due to an...interesting 10 meter trip through a hangar that occurred when she tried to operate a helicopter as a young girl.
In the fight against the Behemoth, uses her summoned tentacles to throw Mao into a pile of debris, almost effectively taking her out of the fight.
In the Martial Arts Takeout Race, loses control of her newly made Torrent of Debris spell.
Before getting one of Persephone's peaches, she spends a lot of the fight against Poseidon being rescued by the older, human martial artists.
Niamy of Fuck The Jesus Beam decides to deal with the Bombignat threat by releasing O.B.A.M.A. from his prison, despite him having started 95 World Wars as president and, as it is later revealed, being the source of the Bombignats. Upon his release, O.B.A.M.A. says that he will reclaim his domain, and takes control of the Bombignats.
While not much of a hero, Vash of Christian Humber Reloadednote A crossover between too many works to list here kills a dragon named Le-Hung Doe as part of atoning for killing another dragon, but learns that by killing him, he has started a Ying-Yang War, in which he must fight demons without weapons.
The Prayer Warriors have killed many people in their fights against the Greek Gods, Hogwarts and Communist Russia, but it's implied in The Titans Strike Back that their infiltration and destruction of Hogwarts resulted in many Christian deaths, and now that the school has been re-established, they're going to deal with it differently this time.
The God Empress Of Ponykind: Celestia kills King Sombra. This allows him to ascend and become a Daemon Prince and pull the Crystal Kingdom into the Warp.
Horseshoes and Hand Grenades: Ryusei's attempts to save his friend from the coma by killing Gentaro only made Ophiuchus resurrect Gentaro as a Serpent-bearer with a vengeance to kill his former friends. Moreover, Jiro died anyway, and was resurrected by Gentaro to serve him and kill Ryusei. And that's not talking about how this derailed Gamou's plots for the Day of Awakening and how his benefactor Tachibana—Virgo Zodiarts—has to start injecting Cosmic energy into innocent kids to make up for everything. Was killing Gentaro worth all of this in the end, Ryusei?
In The Swarm Of War, after the Kingdom learns about the Zerg and misidentifies them as a Chaos corruption, a decision is made to bring out the hidden superweapon: hibernating Space Marines. Unfortunately, nine of them are corrupted by Chaos.
While Naegi has plenty of these in And Again, Monobear explictedly points out one to him near the end: his decision to send the strongest students off to supervise Mukuro retrieving her arsenal from her room.
Monobear: What a great idea! Send all the strongest of you bastards away! Defend everyone else with the power to sing and have rich parents! What was your talent again, Naegi-kun: Super High-school Level Strategist?
In Light and Dark The Adventures of Dark Yagami, the girl from the bus kills Dark and gets hailed as a hero for doing so, but he goes to the Shinigami world after dying, kills Blud and becomes king of the Shinigami. He even thanks her for killing him and enabling his ascent.
In The 10 Doctors, the entire reason the Time Lords lost the Time War is that the Valeyard — who the Time Lords created in the first place — killed Damon before he could give the Daleks' attack strategies to the Eighth Doctor. If this hadn't happened, the war would have been much less destructive, the Time Lords and Gallifrey would still be around, and the events of The End of Time would never have happened. Essentially, it's the Time Lords' own fault they got into the Time War, which isn't too surprising.
Later, the Tenth Doctor finds the relevant data spool. He reluctantly decides against giving it to the Eighth Doctor, in order to keep history on track.
In Outrage, the Sixth Doctor reveals Jem's secret identity to Rio Pacheco. Rio doesn't take it well.
In Seeds of Destruction, the Fifth Doctor lands on a lush garden planet, ignoring Peri's request of Pasadena, California. Said planet turns out to be the deadly planet Kryn.
In A Time To Kill, the Tenth Doctor completely shatters James Bond's cover, and the spy is injured in the ensuing fracas.
Game Theory has quite a few examples. The two most notable are Chrono assuming that Nanoha was working with Fate and attacking her in her home, which led to her actually deciding to help Fate fight the TSAB, and Nanoha's consequent decision to help Precia revive Alicia.
In Chronicles Of Harmonys End, Array conspires with Discord to overthrow Harmony (the only force keeping the two of them in line), believing he could destroy Discord himself. He was wrong.
Inner Demons: If Celestia had told Twilight about the prophecy sooner, or broken the news to her differently, it's possible that perhaps Twilight's transformation into the Queen of Darkness could have been slowed or altogether prevented. At the very least, Twilight wouldn't have freaked out and turned Celestia to stone in a fit of anger at the revelation.
Twilight actually pulls this on herself. After the above incident, she convinces her friends to lock her up in the library basement while Rarity searches for a way to stop her descent into darkness and free Celestia. Unfortunately, since Spike is busy helping Rarity and Twilight's all alone, there's no one to wake her up from her nightmares, wherein the Queen persona consumes her completely.
A little later on, Sweetie Belle is on the verge of a Heel Realization, when Rarity's unfortunate wording during a conversation hits an emotional trigger Queen!Twilight had previously planted, causing Sweetie Belle to fully embrace her Face-Heel Turn and reject Rarity as her sister.
Ditzy Don't: Twilight's attempt to help Ditzy by implanting magical copies of the Mane Six's personalities in her head first causes her to outclass Rainbow Dash to the point of her public humiliation, then all the group's negative aspects (Fluttershy's sudden rage, Pinkie's personalities, Twilight's obsessiveness, etc) take over, making her go crazy and chase after Rainbow Dash to force her to let her take care of her.
Rolling in Beaches: Wavedancer taking the Rainbow Pearl out of curiosity (and then keeping it to get close to Spike), leads to it being stolen by the Scaly Back River dragons, who in turn break it and accidentally release the Rainbow of Darkness.
The flashback at the beginning of Atlas Strongest Tournament incorporates the story of Tithonus, with Celestia as the guilty party.
When Rarity saw Ran Biao and Razorwing together, she ran away at the perceived betrayal, which led to Razorwing raping Ran. This led to the breakup of their friendship.
Fluttercruel honestly just wanted to teach Fluttershy something important for her own good, to let her learn the cruel part of nature, but it ends up corrupting her for real as opposed to being just brainwashed by Discord. Fluttercruel is absolutely horrified realizing this.
She also gets Fluttershy, and herself, drunk, which Word of God admits may have had something to do with their behavior following and made Fluttershy more vulnerable to the darkness than she otherwise would be.
While it's Loose Canon, it's implied that the Mane Cast are, unknowingly, being manpulated into commanding Princess Gaia's army via a boardgame they're playing with Gaia herself. If this is believed, Rainbow Dash unwittingly guides Gaia's army into "Gaiafying" Gilda.
If this is true, it is quite possible that Trixie and Twilight Sparkle are unwittingly providing a front for Princess Gaia to brainwash their own mothers into being her knights.
In the aftermath of a battle, your friend-suddenly-turned-enemy lays indefinitely helpless before your group. To help console each other on this tragedy and related circumstances, one mentions that it is not too late to restore or redeem this friend. If you think that taking matters into your own hooves and executing your petrified former friend, Discord, by pulverization is not a logical next step, you are smarter than Galaxia, whose deed costs her life, sets the stage for a 1000 years of tyranny, and worst of all, could have been easily avoided.
During the battle between the Dark World!Elements of Harmony and Discord's remaining minions, Spike has to choose between helping Rarity and Twilight, both of whom got separated from the main group while fighting Fluttercruel and Angry Pie (respectfully). He figures Rarity will need more help and goes after her; in fact, not only has Rarity by this point killed Fluttercruel, but Twilight ends up overpowered by Angry Pie, who rips out her Element and leaves her for dead.
In Secrets and Lies, Twilight tries to prevent Discord from escaping without alerting anypony who doesn't need to know what's going on, in order to avoid triggering mass panic. On top of this, she's keeping other secrets from her friends, and her attempts to fix everything without revealing them lead to terrible complications. Her biggest break, however, is when she determines the best way to help Fluttershy is to have her commited, leading to her getting dragged away kicking and screaming and locked up in a madhouse.
In Screwball Over, Twilight Sparkle and friends discover that their attempts to cure their friend and neighbor Button Stitch of her tendency to turn into her Toon Physics-powered alter-ego Screwball were all part of a plot by Discord to summon an endless swarm of mini-Screwball clones and swamp Equestria. Discord, having been turned back into stone at this point, has left a message mocking Twilight for falling right into his trap with her goody-goody ways. Twilight is only saved from a Heroic BSOD by the reassurances of her friends and the princesses that she shouldn't blame herself.
Pulled on the readers in Dungeon Master Bonbon. When Lyra temporarily takes over the blog, they spam her with asks saying how Bonbon loves her, causing her to break up with Bonbon out of fear she's leading her on.
Escape from the Hokage's Hat has Shizune not let a recovering Naruto (who just wants to provide support) fight by slapping him with a Interface Screw jutsu. This ends with Hinata (literally) getting stabbed in the back, Shizune too tired to heal Hinata while the enemy attacks, Naruto using a Forbidden Dangerous Technique that could've fried his charka network to save them and her losing Naruto's trust. She, however, at least notes how she screwed up and starts fixing the mess.
Everything in Imperfect Metamorphosis can ultimately because of Team 9, and Cirno specifically. They were responsible for both releasing the Shadow Youkai and getting Yuuka involved, and their constant meddling continued to make things even worse. Other characters caused a lot of headaches too (especially Eirin and Yukari), but nowhere near to that extent.
Okay, Luminosity's only difference is that Bella's a different character, so naturally the differences for good or ill will be her fault...village murdered because of her? And now the Volturi have shapeshifters on their side? Because Bella thought it would help them. Oops. And Elspeth is following in her mother's making-the-Volturi-stronger footsteps.