In the fourth season, Spike schemes to break up the Scoobies by exploiting the existing tensions between the group, and then planting evidence to lure Buffy into a trap as part of Adam's plan. However, after all is said and done, Adam points out that Spike gave Willow the evidence, and Willow won't be speaking to Buffy now. Spike quickly goes out to fix his scheme. Word of God confirms that the writers themselves didn't think of that either and didn't realize their error until it was time for the next episode to air, so they added in Spike and Adam's exchange rather than rewrite the entire previous episode.
In the sixth season, magic was portrayed as akin to a drug, which was highly dangerous and addictive, and could even lead to users becoming "junkies" willing to do anything for a "fix," as happened to Willow slowly over the course of the season. Joss Whedon himself didn't like this development, and fans agreed; season seven's first episode featured a scene where Giles explicitly states that magic is not addictive, and it's explained that Willow's actions were actually due to her not using magic.
"The Girl in Question" was reviled by the fans for many reasons but mostly because Buffy was revealed to be dating an unseen figure named "The Immortal" who happened to be an old rival of Buffy's previous lovers Angel and Spike. This was for a long time the last thing known about her in the entire Buffyverse. The comic continuation revealed that this Buffy was actually another slayer impersonating her and that Andrew Wells lied to Angel and Spike as a prank.
The later seasons of Buffy did some Draco in Leather Pants-ing of Spike, as even after his Attempted Rape of Buffy, any criticism of him tends to get met with "he has a soul now". In Angel season 5, he and Angel have multiple conversations on how the evil they did is the only thing that will count and he got his soul for a woman, not because of any goodness.
Power Rangers Dino Charge: One of the complaints from Power Rangers Samurai was that the Samurai Rangers had Mega Mode for use in the Megazord but never explained why the Rangers couldn't use it in regular battle. So in "The Royal Rangers", Kendall introduces the Dino Drive mode, specifically stating it was just for when the Rangers use the Megazord.
In the first film for Kamen Rider Decade, the very serious and nihilistic Doctor Shinigami suddenly appears, after being Natsumi's rather quirky grandfather for the whole season. Fans didn't understand. So, in the second film, they make him that way again. But this time, they reveal that he's under the effect of a "Doctor Shinigami" type Gaia Memory. Which is an obvious throw, as those are introduced in the next, only-barely-related series, Kamen Rider Double.
The series also tried to address the controversy around Tackle, the Second Rider from Kamen Rider Stronger, who was killed off and never officially declared a Kamen Rider, mostly due to the fact that she's a woman.
A month after the Prison Break Season 3 finale, it was announced that, in part due to fan reaction, it wasn't Sara Tancredi's head in the box, and she would be back next season. The other big part of the decision was the fact that Sara had only been killed in the first place because of behind-the-scenes drama between the then-pregnant actress and the executive producers. By the fourth season, everyone was friends again so the character returned. And ironically got pregnant.
The third season finale of Bones, Zack is revealed to have been manipulated into becoming the apprentice to a cannibalistic serial killer, and claims to have murdered a man. During an episode of the fourth season, he says that he didn't actually kill anyone himself, he just told the Gormogon where to find a victim and claims he would have killed the victim himself if the Gormogon had told him to. In his mind, this equated to having done the deed himself.
The Doctor Who1996 TV movie included a scene in which the Doctor says that he is half-human; this was widely disliked and subject to Fanon Discontinuity. To ameliorate this, without upsetting the fans who enjoy this interpretation (Eighth Doctor Adventures doubled down on making him half-human), Moffat has stated that the Doctor did indeed utter those words, very carefully not specifying whether they were true. After all, the Doctor lies. "Hell Bent", the Moffat-penned Series 9 finale, has Ashildr/Me ask the Doctor if he's half-human (it has to do with the possibility that he is The Hybrid), but he only asks her if it matters what he is by way of reply, and the conversation takes another path from there.
In "The Impossible Planet"/"The Satan Pit", the Happiness in Slavery depiction of the Ood as a happy servitor race and the Doctor's acceptance of it as unproblematic were seen by many fans as gross breaches of the series's and the character's usual moral positions. Two years later the "Planet of the Ood"" story returned to the same setting and revealed that the slave Ood were only happy because the evil humans had been lobotomising them, and that the Doctor only accepted their servitude because he was a bit preoccupied with a planet orbiting a black hole and Satan trying to kill them all... shut it.
The Daleks got a multicolored upgrade in "Victory of the Daleks", and the bright, colorful Daleks were presented as what a Dalek would look like forevermore, the "New Dalek Paradigm," as they put it. It turned out even this Narm Charm loving fanbase has its limits. So the next time a Dalek had to be a threat, it was a sorta petrified-looking run-down one with no trace of its original color. Every Dalek appearance since then has had the old bronze Daleks as the vast majority if not the only design. The "New Dalek Paradigm" is apparently still around, but they're taking a backseat to their bronze immediate predecessor models.
A visit to the restored Dalek homeworld of Skaro showed Dalek variants from all across franchise history. The New Paradigm Daleks were not seen in any way, not even as background filler, letting us know they're as good as never having been. (This also constitutes a 'throw' to one problem people had with Asylum of the Daleks - in that episode, the past Dalek variants people got excited for were only seen briefly, in light so low it's hard to tell the old ones from the new. The Special Weapons Dalek, which really got the fandom excited, was especially blink-and-miss. Not so in the return to Skaro - the old Daleks get as much screentime as the current model, with the Special Weapons Dalek getting to be the one to yell "EXTERMINATE THE DOCTOR!" as they mobilized.)
The beginning of "Thin Ice" features the Twelfth Doctor seriously acknowledging and discussing his black companion Bill's fears about encountering historical racism in eighteenth-century London, after the Tenth Doctor's flippant dismissal of Martha's (the previous black companion) similar fears in "The Shakespeare Code" was very heavily criticised by fans.
The treatment given Peri in "Trial of a Time Lord" can be considered an inverted "Author's Ruining Throw": in "Mindwarp" Peri has a spectacular death, having the brain of one of the villains transplanted into her (shaved) head before being gunned down by a horrified ally who liked her, King Yrcarnos, but several episodes later in the season finale this was cravenly undone as having been false evidence, with Peri having run off to be King Yrcarnos's queen instead. This was apparently intended to placate fans who would be upset at Peri's fate, but instead the retcon was decried by almost everyone, including Colin Baker and Nicola Bryant (who didn't even know this had been done to her character until long after the fact), and has been largely rejected by fans.
Lost: The producers originally intended for Paolo and Nikki to be major characters. After a fan revolt, they changed their plans by not only killing off the characters, but doing so in an incredibly sadistic way.
Smallville: Season Seven ended with Lana, having just woken up from a Brainiac-induced coma, leaving Clark a Dear John video expressing her belief that she was only holding him back. However, not only were her fans unhappy with this direction, but her actress had been absent for the final five episodes of the season due to filming Street Fighter: The Legend of Chun-Li, and the recent writer's strike hadn't helped matters either. The very next season, in the penultimate episode of Lana's farewell arc, Tess Mercer reveals to Clark that it was all a lie: Lex's men kidnapped Lana and forced her to make the video at gunpoint in order to throw Clark off the trail. Tess even lampshades the Plot Hole of Lana somehow getting her hands on a video camera right after waking up.
In the seventh season finale of House the title character drives his car through Cuddy's dining room window in revenge for breaking up with him and escaping to a tropical beach. This caused a full-blown fan revolt with claims that House became no better than a psychotic murderous Domestic Abuser and that his stunt could have ended with the deaths of several people. The creators responded to this on Twitter claiming that House had made sure that everyone was gone by looking through the window which prompted the fans to point out that Cuddy's daughter was likely in the room and she wasn't tall enough to be seen. Come the season 8 premiere and we get a scene where House turns himself in to the authorities and explains that he had made sure that everyone in the room had left and that he knew that Cuddy's daughter was at a sleepover. Plus for an added bonus after acting like a idiotic sociopath for most of the seventh season, he gets a Humiliation Conga in jail (being the janitor cleaning up after people intentionally pissing on the floor, for one) and the flanderization getting reversed, becoming more like his season 1 self again; still doing shitty things but a lot of Pet the Dog, especially with Wilson.
For the first three seasons of Star Trek: Enterprise, the show was criticised for wasting the potential of its prequel setting by neglecting the Romulans as recurring villains (rather than properly leading up to the known canonical Romulan War) and instead embarking on a long confused Myth Arc involving a "Temporal Cold War" which soon fell prey to The Chris Carter Effect, as well as for depicting the Vulcans as a race of hypocritical Jerkasses. When Manny Coto took over as showrunner for the fourth season, multiple Saving Throws were given: the Temporal Cold War was resolved in the two-part premiere, a three-part story involved a major spiritual revolution in Vulcan society that brought them closer to the aliens we knew and loved, and a major story arc throughout the season involved a resurgence in Romulan aggression which also served to forge alliances between the future founding members of the Federation. The Enterprise relaunch books manage to take this even further by retconning Trip's death into a faked death, as well as dealing with the Romulan War and founding of the Federation.
Dr. Bashir of Star Trek: Deep Space Nine was never the most popular character on the series. With a personality that seemed to vary from episode to episode, inconsistencies with his background, and the infamous "Mistook a preganglionic fiber for a postganglionic nerve" error (Which is akin to an engineering student mixing up a wrench with a screwdriver). So midway through season 5, the writing team rolled out a full-on Retcon to explain it all: That he was an Augment, an illegal product of genetic engineering. And that he'd been acting the fool to fly under the radar. Unlike most retcons, it worked. With the Bashir for the remainder of the show being much better received by fans.
At the end of Season 3 of The Mentalist, Jane kills Red John and sits peacefully waiting to be arrested. In the first episode of Season 4, it turns out that that wasn't Red John and he's found not guilty in a spectacular example of Hollywood Law, so the series can continue as before.
In the fourth season, Sam was revealed to be in a sexual relationship with the demon Ruby. Even putting Shipping aside, the fanbase took a major issue with this. As Ruby was a demon with no corporeal body of her own, she had to possess another woman to use for her, uh, interactions with Sam. By having sex with her, Sam was either raping the host (who had not given consent) or engaging in necrophilia (if the host was a corpse). The writers took a third option by revealing that Ruby's host was a comatose girl about to be taken off life support, whose body was still alive but spirit had moved on to the afterlife. Mileage varied as to whether or not this made the situation any less squicky.
In later seasons, the show began to place more and more focus on the Dean and Castiel relationship, including deliberate subtext and occasional jokes that their friendship is not entirely platonic. Some in the fandom took this as a possible legitimate intention on the writers' part to foreshadow an actual romantic relationship between them, and were extremely excited at the prospect of the protagonist of a very popular, mainstream, genre show being openly bi. However, during season 9, one of the writers on twitter revealed that Dean being bi was an interesting idea but that they had absolutely no intention of making it canon. This caused outrage from people who claimed the show had been queerbaiting - deliberately enticing queer audience members to keep watching with the promise of dearly needed representation without any intention of actually following through. During season 10, therefore, the authors tried to smooth things over with the episode Fan Fiction, in which Dean encounters Destiel shippers and states that while it's not the right interpretation, it's totally cool that they have their own interpretation of things. Reactions to this were mixed - some shippers liked it, but those who really wanted Dean to be bi were only the more convinced that the writers never understood why people wanted Dean to be queer so much in the first place.
In the crossover movie between Tensou Sentai Goseiger and Samurai Sentai Shinkenger, we're given the first cameo appearance of the Kaizoku Sentai Gokaiger, who transform into all Red Rangers. However, it's revealed in the first episode of Gokaiger that the only reason they could do that was because of the Ranger Keys, which they wouldn't get until the time between Gosei and Gokai. How do they solve that? Reveal that the team had been sent back in time on a mission by Domon of the Mirai Sentai Timeranger and they decided to give the two teams a hand while no one was looking. On the other hand, we're still not sure how it is that the Gokaigers keep their ability to turn into other Rangers after the past Rangers' powers were restored at the end of the regular series. Not that anyone is complaining.
Once Upon a Time: Season 5 fixed many problems fans had with earlier seasons. It kept the focus on the main cast and stopped the new characters being a Spotlight-Stealing Squad as fans had been complaining about in previous seasons, fixed some plot holes, and made Belle more than just Rumplestiltskin's Satellite Love Interest. It also acknowledged that Rumple and Belle's relationship had turned toxic and become a Yo Yo Plot Point. The finale threw the biggest though; after years of Regina been seen as an Unintentionally UnsympatheticKarma Houdini that showed no remorse for her actions as the Evil Queen, Regina reveals that her previous lack of remorse was due to repressing it and her entire character arc in the finale revolves around her desire to be free of the baggage that comes from her actions. She then splits herself into her light and dark sides leaving us with a good Regina that can have a fresh start and the Evil Queen who can receive proper punishment.
The Community episode "Repilot" dismisses the entirety of the widely-hated Season 4 (the only season not overseen by Dan Harmon) by claiming that the school had suffered a massive gas leak, explaining everyone's inconsistent and decidedly Out of Character behavior.
Glee removed the new members of the Glee Club in Season 5 because of the fans who hated the new characters and direction old club members had taken. Instead, the show began to focus on what the old cast was doing out of the club.
In Isabel, the stylism of Ferdinand and Isabella resembles their real counterparts historical portraits more in the second season than in the first. Ferdinand grows his hair to mid-length (although actor Rodolfo Sancho never shaves his beard) and Isabella starts using a white cowl after suffering a miscarriage in the season premiere (which fits well with white being the color of mourning for late 15th century queens). The latter was an explicit answer to critics who claimed that the show had modernized Isabella's look too much.
The first season of Better Call Saul ends with the revelation that Jimmy's brother Chuck has been actively fighting his efforts to get a real job as a lawyer. This led to a lot of fans stating that if it hadn't been for Chuck's sabotage, that Jimmy would have never become the amoral Saul Goodman. The writers disagreed and had Jimmy change his mind about taking a job that Kim and Howard had arranged for him with a different firm (in the first season finale he had given up on his legal career and was planning to go back to being a con-man). It quickly becomes obvious that Jimmy never could have made it as a straight-arrow lawyer, and he's back to his old tricks a few episodes later.
The third Midnight Caller episode was heavily criticized by LGBT and HIV/AIDS advocacy groups for its portrayal of a bisexual man who knowingly infects people with HIV. While researching the follow-up episode, "Someone to Love," writer Stephen Zito talked to some of the people who protested "After it Happened." He and guest star Kay Lenz also talked to a support group for women with AIDS, and some of their stories were used in the episode. As a result, "Someone to Love" was much better received, and was praised by many of the people who had criticized "After it Happened."