Early in the third season of the main Adventure Time TV series, Princess Bubblegum unambiguously and permanently shuts down Finn's vague adolescent romantic feelings for her by saying that the gap between his age of fourteen and her (apparent) one of eighteen is too big. Ryan North's official Adventure Time comic spin-off later gave the Fubblegum shippers some support by revealing that in an otherwise Bad Future Finn and Bubblegum are lovers, and having her explicitly say that now Finn's a grown man in his twenties a four-year age gap doesn't mean much. A second, entirely different potential future seen in a later arc also had Finn and Bubblegum married, although in a three-way marriage with Marceline.
The main comic series has done this in season 10 several times, usually aimed at season 6 of the show. When fighting the Soul Glutton Spike asks to be immediately staked if his soul is destroyed since he'll go back to being a souless monster, refuting a lot of his pre-Season 7 character development and even claiming he couldn't "really" love Buffy before the soul (this coming from a character who is primarily defined as being "love's bitch"). Similarly Buffy outright tells Spike she was never upset with her friends for bringing her back to life in season six, but upset with herself for being upset and missing heaven. This has caused some serious Fan Wank as Spike being able to love Buffy even without a soul and Buffy being upset at the Scoobies for pulling her out of heaven were very common interpretations.
A major part of the "Vengeance" arc is discussing the idea that Spike puts the women he cares for on a pedestal and then forces them to push him away so he doesn't have to break up with them. Given this is the vampire who was slavishly devoted to Drusilla for over a hundred years and only broke up with her after she cheated on him repeatedly and refused to be with him and he never had anything resembling a high opinion of Harmony, and his famous "you're a hell of a woman" speech to Buffy it has been a contentious move. And then Spike, the man who has gone to ridiculous lengths to both prove his love and not be broken up with, gets it in his head that the way to break the cycle is to try and break up with Buffy just so she can call him out on it.
The comic Spike: Shadow Puppets plays with this trope by having the Japanese Smile Time puppets literally armed with the Smile Time Official Cannon. Spike barely dodges the blast and gingerly gets to his feet, muttering, "I hate the official cannon." Hey, after the way it kicked him around, who could blame him?
The people responsible for the Angel: After the Fall comic at IDW were pissed at the people responsible for Dark Horse's Buffy the Vampire Slayer comic for the reveal that Angel was Twilight. So much so, they created promo pictures for their new Spike series wherein Spike burned a Twilight mask while saying, "He's definitely not Twilight."
In the early 1990s, the comic strip had a period of Seventh Doctor strips explicitly sharing a continuity with the Doctor Who New Adventures spin-off novels, including the novels' original companion Bernice and darker aged-up version of Ace. However, when a new editor who strongly disliked the New Adventures was appointed, the strip moved to a run of stories featuring various earlier Doctor-companion teams. The last of these, the climax of a multi-story arc that led into the first major arc of the Eighth Doctor strips, featured the Seventh Doctor and the younger Ace from the TV show, and shockingly killed her off at the climax. This was widely seen as an aggressive attempt to knock the New Adventures tie-in strips out of continuity. Following the series' return to TV, the comic's made mention of strips both during the tie-ins and after the split, but then "Who" is the series that gave us the Timey-Wimey Ball...
One of the aforementioned "earlier Doctor-Companion team" stories, "Change of Mind", which features the Third Doctor, Liz and UNIT, and is explicitly set after Liz's resignation, begins with a caption bluntly stating a date in 1971, establishing the strip's view at the time on the UNIT dating controversy.
In the early Doctor Who (Titan) Eleventh Doctor comics, there are a number of scenes involving the Doctor's highly-combative companion Alice that make it very clear that the writers, Al Ewing and Rob Williams, are not at all happy with Doctor Who fans and writers who think that the Doctor being an Insufferable Genius is cool or admirable.
Lauren Beukes's Fairest arc "The Hidden Kingdom" contains an approving line about herbal abortifacient preparations that seems thrown in solely as a slap at the anti-abortion subtext (and outright text) that appears at times in the main Fables series.
For decades Red Sonja's backstory included that she was granted her fighting skill by a goddess on condition that she not sleep with any man unless he first beat her in combat. So it went until Gail Simone took over in the Dynamite run and introduced Osric the Untouched, a male swordsman under the same condition. Sonja promptly calls it out as stupid, explicitly jettisoning it out of her past.
Sonic the Hedgehog (Archie Comics): The feud between writers Karl Bollers and Ken Penders tended to come down to this, with them retconning each other's story ideas in favor of their own all the time. Of special note is Antoine's attitude change after the Time Skip: Bollers wanted it to be natural Character Development, and it would have been the lynchpin of several ideas he had planned for later on. But Penders disliked the change, so he made it that Antoine had instead been switched with his Alternate UniverseEvil Twin.
And then, both of them then left the comic at the same time, allowing new writer Ian Flynn to scrap the majority of their ideas and replace them with his own...kinda. Actually, it's not as simple as that: with the bridges between Penders and Archie/Sega permanently burned, the writer ending up launching lawsuits concerning the characters and concepts that he created, stating that belonged to him and for them to be removed from the comics. They eventually lead to a settlement that, in part, had Flynn use the ending of Sonic the Hedgehog/Mega Man: Worlds Collide as a Cosmic Retcon for the series, in order to remove every element that Penders created.
After a long and well received run co-writing Strontium Dog with Alan Grant, John Wagner left the strip with Grant; who promptly killed off all the main characters. Skip forward a few years and Wagner resurrected the strip, declaring the last twenty years of comic null and void. The official line is that those stories were "the legends of [main character] Johnny Alpha and the new stories are what really happened". Cue lots of fans shouting Nooooo! in unison. Wagner went back on a lot of this later, with "The Final Solution" actually being mostly declared canon again.
The website "Comic Book Resources" has a series of Armed With Canon "meta-messages."
It addresses the library ghost, Eleanor Twitty, as seen in the first act of the original film. The Ghostbusters are never shown catching the ghost in the film, so Ghostbusters: The Video Game (which the IDW comic largely treats as at least partially canon), allows the player (and the Ghostbusters) to finally catch it. This takes place in 1991, 7 years after the events of the first film. The Ghostbusters never bothering to catch the ghost until then makes them seem like huge jerks (considering it was their first ever ghost sighting and gig), though Ray implies they'd tried to catch it more than once. Year One reveals they caught it offscreen during the second act of the first film, after the library staff personally showed up at their door to complain, meaning it was released along with all the other ghosts when Walter Peck had the containment unit shut down, resulting in the Ghostbusters having to catch it again.
It retcons the sleeping pills Venkman uses to sedate Dana Barrett (when possessed by Zuul) as belonging to Dana (she claims she was taking them for hiccups). This is presumably due to 1) some claiming Unfortunate Implications about Venkman carrying around sleeping pills to give to women and 2) The fact that the doze he claimed to give her was absurdly inaccurate, although he may have just been joking on that part.
And that's without even touching the topic of the Stay Puft Marshmellow Man, whose status as both a form of Gozer and its own separate entity comes up in the franchise from time to time, including the IDW ongoing, the IDW "Infestation: Ghostbusters" miniseries (in which it's revealed the latter version can be caught in the ghost traps), and Ghostbusters: Afterlife.
Alan Moore's first issue of Supreme gives the series a complete Continuity Reboot, and shows the existing supporting characters of Lady Supreme and Kid Supreme now happily living in the alternate dimension of the Supremacy after being Ret Goned; Kid Supreme is also shown to be engaged to a 1940s-era sidekick called Sally Supreme. However, the fourth issue of Kid Supreme's own spinoff titlenote (ultimately never published as Kid Supreme #4 as the title was cancelled, but instead included in the Anthology ComicAsylum issue #9) shows him trying to escape the Supremacy after finding out the decision to stay was forced upon him, being attacked by Sally Supreme for attempting to leave, and finally diving through the golden gateway back to Earth with seconds to spare before it closes.
of Armed With Canon "meta-messages."
Unfortunate Implications about Venkman carrying around sleeping pills to give to women and 2) The fact that the doze he claimed to give her was absurdly inaccurate, although he may have just been joking on that part.