The episode "Hurricane Fluttershy" had a flashback to Flight Camp when Fluttershy failed a flying test and crashed, after which she was surrounded by her class mates and subjected to a Circle of Shame. This makes a similar flashback scene in Getting Back on Your Hooves, where a near identical incident happened to Rainbow Dash, not only plausible, but even more disturbing. Even the author was a bit freaked out by this.
At one point in "The Crystal Empire Part 2", Twilight uses dark magic, which causes her magic to go from magenta to black, to find a secret underground staircase made by King Sombra. In the fanfic Pages Of Harmony, written several months before The Crystal Empire aired, Twilight's Mad Scientist Laboratory is reached through a staircase very much like Sombra's, and her magic's color changes from magenta to black.
The Fanfic Trixcord involved Trixie, after being terrorized by Discord, run into an open street where she gets her neck snapped being run over by a carriage (she gets better). The episode Magic Duel had an insane Trixie with semi-fourth wall breaking powers declare she did not trust wheels.
In Little Sun, Twilight chews out Princess Celestia for ordering the murder of Applejack's parents for being part of the Nightmare Cult, saying that Apple Bloom was only a few months old then and has no memory of them. It became harder to swallow after the San Bernadino shootings in December 2015, in which the married terrorist couple responsible was killed in a police shootout and left behind a six-month-old baby girl (who may or may not have been an alibi).
In Comatose, Shining Armor has a nightmare where he witnesses his own harsh words toward Twilight in "A Canterlot Wedding", and he is unable to move or be heard to try and stop it. A similar nightmare would befall Sweetie Belle in "For Whom the Sweetie Belle Tolls".
In chapter 75 of Child of the Storm, the usually nigh-infallible and apparently omniscient Doctor Strange, when questioned by Jean on whether he's correct about something, makes the following Badass Boast: "I am the Sorcerer Supreme, Miss Grey. Mistakes and misapprehensions are for other people." However, chapter 9 of the sequel, Ghosts of the Past, reveals that he previously made one hell of a mistake, his inability to track Sinister meaning that he didn't arrive in time to stop him stealing Maddie/Rachel from her crib.
In chapter 2 of Ghosts of the Past, Harry snarks - when Carol grabs his arm, intent on hauling him Slurpie-wards - that he'll have to follow, because, "I'm very attached to my arm and I like to think that it's very attached to me." In chapter 14, his Blank Slate body, the Red Son, winds up having his left arm - and eye, and most of his left side - blasted off by Magneto as the latter tries to bring him down without doing permanent damage, then replaced with a Cable style techno-organic arm.
While not noticeable to the reader at first, the scene in Nexus where Dante hugs his nephew could count, especially if you read the precursor’s bittersweet ending. It was Heartwarming Moments, since the character showing the emotion was Dante, until Jack ruined the moment by (unknowingly) reminding Dante that he didn’t remember him at all. Then Dante just looked depressed.
The Katawa Shoujo fanfic From Shizune's Perspective was written before the release of the full game. Several of the twists come off in a new light when you consider what happens in Shizune's route.
Early on, it's revealed that Shizune is bisexual and Misha is heterosexual; Shizune mentions that she once confessed to Misha, but takes her rejection due to Incompatible Orientation in stride. In the full game, the situation is reversed; the lesbian Misha confesses to the heterosexual Shizune, and is rejected, but Shizune wants her around as a friend, leading to tension as Hisao gets closer to Shizune.
Midway through the fic, Shizune finds out that Misha and Hisao are in a relationship when she finds them having sex, and is upset because they never told her. In the game, choosing to give Misha Sex for Solace gets you Shizune's bad ending, and Shizune never even finds out.
Later in the fic, Shizune vents to Emi about how her deafness prevents her from getting school gossip, which, in serving as Student Council President, earns her a reputation as bossy. In the full game, Shizune's well-intentioned efforts to inspire the student body to act, hampered by her communication problems, drove the rest of the council besides Misha away, and resulted in her being quite lonely.
In Superman fanfic Superman of 2499: The Great Confrontation, starring the descendants of Superman and Supergirl and written in the early 00's, the arguments of the side of the Family that argues against revealing themselves to the world no matter what is usually treated as strawmen. Several years later New Krypton came out and proved humans were willing to accept the existence of a Superman, and even a Superboy or a Supergirl... but they would never accept hundreds of Kryptonians living among them.
In DC Nation, issues #20-#21 of the New Teen Titans comic (May-June 1986) are affectionately known as "The Mission from Hell." The Titans were (temporarily) mostly broken up after incidents involving or happening roughly around the time of Crisis on Infinite Earths. Wonder Girl, who is left in charge with an empty nest, calls in Aqualad, a newly-minted Flash, a Hawk without Dove, Jason-Robin and her ex-boyfriend Speedy. At the request of King Faraday, they help to protect a peace conference which is being threatened by Cheshire. Yes, the Cheshire Speedy had a relationship with. This was where it was discovered they had a child together. Issue #21 closes on some supposed to be heart-warming reconciliations between Terry Long and Wonder Girl and also Speedy and Cheshire, including him getting to hold his daughter for the first time. Also, Wally getting to explain his new role as The Flash to his hero-avoidant then-girlfriend Francis Kane. Now, look at these events through the lens of:
Wonder Girl and Speedy still being in love, but not pursuing those feelings due to the machinations of Dark Angel.
Aqualad being suicidal after the loss of Tula.
King Faraday being mind-controlled by Diablo to be Gamemaster.
Wally-Flash not knowing what he's doing and trying to imitate Barry Allen. His behavior around this time is often-cited by his peers in-game as to why "growing up and becoming JLA members" is no longer concidered an option if the Titan in question wants to keep their sense of self.
Wonder Girl having a miscarriage after a fight with Cheshire when she hadn't known she was pregnant which actually stopped Aqualad from killing himself. After getting treatment, which she swore him to secrecy about, the next day she finds out about Lian's birth.
Jason being the voice of reason among his older, more experienced peers. In Nation-canon he received a statue in the memorial hall upon his death for this and the work to free Raven, which is different from in pre-reboot DC-canon.
Having Speedy, Wonder Girl and Flash return to Cheshire, Terry Long and Francis Kane with the idea that this is a relief to them. In Nation, all three couplings have been portrayed as abusive and/or unhealthy relationships.
Realizing that Lian would have been conceived just about the time of Wonder Girl's wedding to Terry Long with the compressed timeline. Can you say rebound?
In The Prayer Warriors, during the attack on the temple of Zeus in "The Evil Gods Part 1", Percy Jackson encounters a woman being raped, killing her rapist but sparing her because she cried out loudly enough and indicated that she was not enjoying it. In "Threat of Satanic Commonism," when Ebony gets raped, he not only kills the rapist, but also kills her, showing that he meant what he said.
In How I Became Yours, Toph - after hearing that Sokka revealed Zuko and Katara's love child Kuzon's existence by sending a letter to Zuko - says, "Katara is going to kill you... I can only imagine what Mai will do to Zuko...". A demonized, Out of Character, Yandere Mai poisons Katara, causing her to miscarrynote it had happened at the time, but Katara was unaware of Mai's involvement at this point in the story, and later tries to kill her herself.
In the sequel comic Rise Of The Agni Army, it's pretty much a given that Zuko's murderer was indeed Mai, who somehow survived being bloodbent to death. Brr...
It's astonishing how similar Zuko confronting Mai about hiding the existence of his love child with Katara by hiding her letters until a servant showed them to him is to Ozai confronting Ursa in a flashback in The Search over Zuko being Ikem's son rather than Ozai's, something he learned by the servant Ursa entrusted to deliver her letters betraying her and giving them to Ozai. Zuko may be turning out more like Ozai than he thought here.
There's bucket loads of Foreshadowing for the season 1 finale of Children of Time, and plenty of moments within the three-part finale itself that get worse later on.
“Not if you do not wish to truly experience your role and sleep on the street...” Which Beth Lestrade actually ends up doing in the next episode while on the run with the Irregulars.
“I should have cuffed you to the railing back at Baker Street.” Sherlock Holmes cuffs Beth to the cab door just half an hour later, which starts the ball rolling on a world of trouble between the two.
Not to mention the use of Vincent Starrett's famous Sherlockian poem as a Motif for the finale. Sherlockian readers will never think of the words "always 1895" the same way again.
In The Spoils of War Bellatrix declared when she was six that one day she'd live in the biggest castle in the world. When Harry and a sane Bellatrix review her memories, she notes she was right. The biggest castle in the world is Azkaban.
In an author's note for the fanfic New Lifenote Which, just as a warning, has a pairing that many people would consider Squick the author mentions that he is serving in the Canadian military, so updates will be sporadic because he doesn't have access to a computer. A review dating from June 2, 2010 sends well wishes to him and hopes that he will recover. Sadly, the author later died from injuries sustained in Afghanistan.
Note that as of 2014, the author's cousin has deleted all of the chapters to the story except for the first one, but the reviews still provide evidence for this.
In Thrones of the Four Pillars, the Ghibli Hills is a Miyazaki-themed world that is destroyed by the Big Bad. This gets harsher when it was noticed that Studio Ghibli closed its doors (it went under restructuring process though but it doesn't make it less harsher).
In the Gensokyo 20XX series tie-in the Gensokyo Diaries, Sanae mentioned, in her second entry, that Kanako slapped her (for reasons unknown, be noted). If we consider what happens in her last diary entry before her death in 20XXI, the latter's abuse may have had its roots there. Likewise, we have Reimu's diary, as those were her last rational thoughts pre-age regression.
In Pokè Wars: The Subsistence, after fending off a pack of bloodthirsty Fearow, Tracy says "I hope that Ho oh wasn't affected by the dampener removal, I'd hate to see such a great Pokémon like that do terrible things." This gets harsher when it is revealed that not only was Ho-Oh affected by the dampener removal, he was the reason for it happening in the first place. To make this even harsher, his justification for the dampener removal? Genocide of the human race.
Harry Potter and the Boy in the Flowerbed, which was written before Half-Blood Prince and Deathly Hallows came out, explores George's (and to a lesser extent, Fred's) failed attempts at getting their Apparition licenses. They managed to Splinch themselves (leave parts of them behind) during at least a few of the attempts, though it was Fred that lost an ear.
In a more disturbing fashion, Chapter 8 of Magna Clades shows the main antagonist Zoisite raping an underage Connie in graphic detail, and the very next chapter has an Author's Note dedicated to Justin Carmical, who'd killed himself that year in 2014. Four years later, he was posthumously revealed to have sexually groomed underage girls while still a producer at Channel Awesome. Yikes.
The End of Ends: Count Logan became an omnicidal villain simply because he was dumped and because he had a tragic past that the author exaggerates by making it seem like nobody liked him, not even the Titans. A few years after this fic was written, Elliot Rodger would kill 6 people and himself because he was enraged that he was a virgin and had a sad past consisting of...watching other people make out and listening to other guys brag about their sexual exploits. He would also write a manifesto stating that he'd like to have women almost completely exterminated and that he intended to kill many more people on his "Day of Retribution".
Super Sentai Vs Power Rangers The Liveblog: any moment where main character Rika berates the story about how Cole was chosen to become Red Conqueror and how his shipping with Sakura was handled, coupled with the potshot against the events with Sean's ascension as the Ultimate Red Legendary Ranger and using some certain Twitter posts to disprove Cole's kindness towards women, became this with the news that Rick Medina (Cole's actor) stabbed a roommate with a sword and killed him.
In The Citadel Of Truth, when Finn reunites with his parents in the afterlife, they are presented as a loving and caring parents who sacrificed themselves for the sake of their son. It makes the revelation of who Finn's fathertruly is in the canon Adventure Time even more heartbreaking.
The Fan FilmBatman: Dead End features the Joker being lifted up and dragged away by a xenomorph, never to be seen again. Andrew Koenig (the actor who played the Joker and son of Walter Koenig) died by hanging himself.
In Feel, we have the resident Ill Girl Rei and in the chapter after her POV, where she was talking about the first time Satsuki spoke and how Satsuki worries about her and her health problems, it is implied that she passed away. Amoridere's grandmother had just passed away and said chapter and the one after was written while she was in hospice, which makes this all the more worse, especially since, shortly after, she had written a dedication to her.
In The Familiar of Zero Louise's classmates mocking her about being a failure was already pretty depressing, but two points in Soldier of Zero make it far worse. First, Louise keeps a stock of Dreamless Sleep potions which at the times she used to deal with odd dreams and nightmares but originally used them as an alternative to crying herself to sleep. Second, in her first year Louise locked herself in a chapel and prayed to God and the Founder for a sign that she wasn't a failure or a mistake. She brought a knife with her with the intention of leaving with her answer or not at all.
The already Tear Jerker worthy backstory for Kurumu in Get What You Wanted and it's spinoffs, being so desperate for Tsukune's love she was willing to be his mistress if he'd just show her some love, becomes far worse with the canon explanation that heartbreak will kill a succubus.
The One Piece fanfic Now We Are Six has the crew encounter odd magic mushrooms that de-age them to six years old, though with their memories intact. While they're cultivating the cure, some of the crew goes hunting and Sanji is angry about his child body being unable to handle the strain. When Usopp chides him for complaining, note that this fic was written in 2012, several years before we found out certain things about Sanji.
Usopp: You know, Sanji, I don’t know what kinda childhood you had, but maybe you shouldn’t be so unhappy you weren’t a lean, mean killing-machine at the age of six. I mean, think about it, for heaven’s sake.
Marie D. Suesse and the Mystery New Pirate Age!: This fic was written long before Trafalgar Law's backstory was revealed, but it still manages to resonate when his crew dies and you realize this is the 'third time his family has died right in front of him. No wonder he went nuts.
"No. Not my family. They're everything to me...I can't lose them."
Law did not smile. "I know."
That Faith clearly uses her sexuality as a shield is harsh on it's own, but in Xendra it's eventually revealed that she was a child prostitute before being Called.
In the Ranma ˝ fic Autumn and Spring which takes place in the distant future, Ukyo is revealed to have also fallen into the Spring of Drowned Girl, and is forced to stay in the cursed state of her younger form when her default body ends up suffering a fatal heart attack, to which Ukyo realizes to her horror if she ever returns to her default body she will likely die instantly. This ended up becoming both far more uncomfortable and tragic when Ukyo's voice actress Hiromi Tsuru ended up dying from a heart attack in November 2017.
In Chapter 61 of Universe Falls, the Gems react pretty badly to learning Rose Quartz had their memories of Ford Pines erased, and why. Then "A Single Pale Rose" aired and revealed an even BIGGER secret Rose had been keeping from them: Pink Diamond is Rose Quartz, and faked her death.