Sometimes, even DMs get railroaded by the publishers who make their cherished games. When the canon plot is going south, nothing works quite as well as taking an entire RPG world off the rails. It's hard to pinpoint what sorts of things people will accept in Tabletop RPGs, but rest assured whenever there's a rules change, someone is going to be unhappy.
The Squats are something of an inversion. The authors hate to acknowledge the Cosmic Retcon, much less the subject of the retcon itself, while fans have turned the retcon into a bit of Memetic Mutation.
Dan Abnett's books (especially Gaunt's Ghosts) are either proof of his reputation as the best 40K author, or dismissed as "him getting high on his own popularity". There is rarely any middle ground on this.
CS Goto (also known as CS multilaser, due to his bizarre affection for the weapon) is the only 40K author whose works are near-universally declared non-canon amongst fans, due to rampant Canon Defilement and general bad writing.
Damn near anything written by Matt Ward will fall to this, on account of his reputation as a Promoted Fanboy who loves the Ultramarines so much it borders on fetish. Accusations include turning the Ultrasmurfs into the bestest Space Marine Chapter ever (whom every other Chapter aspires to emulate and bemoan their lack of being Ultramarines), ruining literally every codex he has ever written, and every single army he's come into contact with has had its fluff tortured, been turned into an unstoppable table-destroying death-army, or, more commonly, bothnote the exception is the Necrons, the only Matt Ward codex the majority of fans actually like. Amongst a significant section of fans anything the man touches is loathed and ignored, in that order.
Considering both the BA and Necron books were written by Ward, it isn't surprising.
The 5th edition Grey Knights codex, also written by Matt Ward, contains the infamous Khornate Knights incident. Basically, they killed a detachment of Sisters of Battle and smeared their blood all over themselves so that they could acquire a daemon sword, which is bullshit on multiple levels. But anyway, the Grey Knights never would do such a thing, and that never happened. Don't make us hurt you.
The same Codex introduces Kaldor Draigo, the Mary Sue to end all Mary Sues. This is a guy who rampages across the realms of the Chaos gods themselves and carves things into the hearts of Daemon Primarchs with no consequences, and is held up as the defining example of Ward's failure as a writer.
The convoluted attempt to flesh out the backstory of the Necrons from 3rd edition onward has inspired several fans to develop mental blackouts when the words "C'tan", "Necrontyr", or "Old Ones" appear, in response to the overplayed role the Necrons' equivalent of special characters gained in the process. The Necrons themselves faced serious resistance when they were first introduced, as their "armies" at first consisted of a small number of boringly unstoppable robots with little variation and no character.
The Tau were considered by some to be a transparent attempt to appeal to fans of Japanese cartoons, without properly making them fit into the "Dark Future" aesthetic. With repeated Codex updates they have, by 5th edition, lessened this attitude somewhat by revealing they aren't as shiny as they like to appear, along with hints of mind control, mass sterilisation, and Imperium-style totalitarianism.
Its fantasy brother also has an example, the Mechanical Horse unit of the Empire. About no one takes it seriously.
The Old World of Darkness game Vampire: The Masquerade had a supplement known as Dirty Secrets of the Black Hand, which revealed that Tzimisce vampires were in fact infected with spirit-parasites called "soul-eaters"... except for a secret society known as the "True Black Hand." Besides not fitting at all with the themes of the game, this wasn't even an original idea - it was stolen wholesale from Necroscope. Fans refuse to acknowledge this one ever existed, and speaking the name in the wrong place can start a Flame War. White Wolf never officially decanonized it, but the book End of Empires wiped out the True Black Hand and later books dismissed the contents of Dirty Secrets as utterly wrong. Given how often the supplements seemed to contradict each other, everyone had at least one they refused to pay attention to, although seldom with the level of consensus of Dirty Secrets.
While never Word of God, it was a fairly well-known open secret that Dirty Secrets was created without official approval by a disgruntled writer as a Take That against White Wolf management; and its status in canon was never fully accepted.
Another World of Darkness supplement a lot of players prefer to ignore is Mummy: The Resurrection, for the reason that no modernizing can make bandages wrapped around a rotting corpse look good.
This is more a disconnect between the illustrations and the text. A lot of the text seems to suggest that Mummies have their own little version of the Masquerade and look just as human as non-Nosferatu Kindred. Meanwhile the art depicts them as dessicated corpses wrapped in bandages.
Gypsies is also seen as a dark mark for the period and the pinnacle of the Old World of Darkness's tendency for well-intentioned-but-not-well-thought-out multiculturalism. It was all about secret bloodlines of Roma with powers based on deception and trickery. Oh, and it had a power stat called "Blood Purity."
Many players were so upset about the Avatar Storm in Mage: The Ascension that they sent writer Jess Henig death threats (even though he was only following the goals already set out by his immediate predecessor, Phil Brucato), and still have flame wars even today. Not only were these ridiculous temper tantrumscompletely insane from the point of view of any normal human being, but White Wolf had to revise the line because they were losing money. But that's gamers for you: damned if you do, damned if you don't. It's just a goddamn game, for chrissakes!
Some of the tribebooks in the revised edition of Werewolf the Apocalypse disappointed fans. For example, the revised Children of Gaia tribebook drew criticism for its bad writing, and the revised Black Fury tribebook drew criticism for abandoning the feminist themes of the first edition tribebook..
Within the Legend of the Five Rings gaming community, members of the Scorpion clan have mentally written out hundreds of pages of canon material because, as they put it, "First rule of Zombie Shoju: We do not talk about Zombie Shoju."
Many "Legend of the Five Rings" fans also refuse to acknowledge that the Canon Storyline even continued beyond Toturi I becoming Emperor. Even those that won't go that far prefer not to talk about Hidden Emperor.
A large faction of the CCG players considered the game to have ended after it was picked up by Wizards of the Coast, particularly since their first post-acquisition expansion set, "Scorpion Clan Coup", and in particular the Hidden Emperor arc, was seen to have effectively destroyed the game balance. Re-acquisition of the game by Alderac, and the Retcon and banning of the Hidden Emperor factions with the release of the Four Winds sets, effectively restoted continuity.
The fact that the Forgotten Realms setting of Dungeons & Dragons adjusted the metaphysics to fit 4th Edition by killing off the goddess Mystra and destroying the Weave in the process, despite the fact that she had died once and protected the Weave by storing it inside the human wizard Elminster got a lot of 3.x fans pissed.
That's just the tip of the iceberg. There was wholesale deicide that saw not only Mystra killed but a slew of other deities, some of which were also fan favorites, many by virtue of Idiot Ball. The demihuman pantheons received the worst culling, most notably the Drow pantheon, which got whittled down to Lolth and saw Ensemble Darkhorses Vhaeraun and Eilistraee get killed off in a trilogy of poorly-received novels (the former was killed off-screen, and what became of the latter's followers was rife with Unfortunate Implications surrounding race). Bear in mind that there's still a loud but vocal minority in the FR fandom that consider the first, comparatively less severe deicide that happened between 1E and 2E discontinuity. And that's before getting into the Time Skip that ensured a number of beloved NPCs were killed off-screen. 4e Realms is a Base Breaker, to put it mildly.
The sheer breadth of the changes (4E changed a lot more than just the metaphysics and the death of a slew of gods, and the 'natural' consequences of a century-long timejump) led some old fans to fanon discontinuity not on the events, but on it being the future of the Realms rather than a new and interesting setting that just happens to use a fair bit of Realmsian names and terminology.
For that matter, there are fans who disregard the existence of any Dungeons & Dragons development past AD&D second edition...
There are fans who prefer to pretend that Thief class introduced to the game in Supplement 1: Greyhawk never existed.
For a work with no actual narrative to it, simply rules content, the Fiend Folio Tome for AD&D can attract something like Discontinuity sentiments. Or maybe everything in it except the Drow and Githyanki. Almost definitely the Flumph. I believe I read somewhere, that if AD&D had gotten to a second edition with Gygax at the helm, the Folio would have been canon discontinuity.
Psionics has a similar effect as well. Simply put, only trolls start threads to discuss its pros & cons since neither camp will ever move, or even just agree to disagree.
Well, this isn't as big a difference as some other examples, since there isn't actual canon for the D&D game, just the campaign settings.
Complete Psionic is one of the only examples of an optional sourcebook receiving this dubious honor. It's a book on psionics, for starters, which already puts it on shaky ground, but it surpasses the mere controversy and occasional brokenness of the original Psionics Handbook it supplemented. The book is about half-finished; several feats and abilities are missing crucial text, the anarchic initiate, meant as a wilder class, is impossible for wilders to finishnote It requires eight ranks in Knowledge (the planes), which isn't a wilder class skill and therefore can't be attained until 13th level, and one of the core classes of the book is actively left out of most of it. The actual material it brings to the table varies from generic and forgettable (a whole load of feats devoted to wasting an action on your mind blade, the lurk, whose entire fluff begins and ends at "rogue who is psychic"note and is actually markedly worse than the other rogue who is psychic) to offensively stupid (the Tier-Induced Scrappy and utterly tone-deaf divine mind, nobody telling the designers that mind flayers don't breed), to the utterly broken (the erudite, which is one of the few classes that can make a wizard shudder with Game Breaker envy). Add in a completely pointless Nerf to the much-loved Astral Construct power, and you have a book where few fans would see a problem in ripping out the ardent's sections and throwing the rest away.
Quite a lot of Mystara fans prefer to believe that TSR's conversion of their favorite game-world to 2nd Edition AD&D was All Just a Dream.
Don't even MENTION the Champions of Darkness Arthaus supplement on a Ravenloft fan forum, unless you want to kick off a three-day slam fest.
Many Greyhawk fans claim that the Greyhawk Wars never happened, or at least happened in a much different way than official TSR canon describes it. Others also declare that the sci-fi elements introduced in modules like Adventure to the Barrier Peaks don't exist and are not part of the setting.
Something that nobody ever seems to understand... the S series modules (Expedition to the Barrier Peaks, White Plume Mountain and especiallyTomb of Horrors) were never intended to be actual adventure modules. The books told you that in the front. They were special convention modules where you were handed a pre-made set of characters and the idea was to live as long as you can. They really are not part of the actual setting.
Zeal does not exist. There are other elements of Exalted that some of the fans prefer not to think about, but Zeal is the one that absolutely everyone agrees on, by virtue of its sheer ungodly brokenness. Void Avatar Prana is a close runner up.
Similarly, no one liked the 1st edition Lunars book, mainly because it painted the entire group as a bunch of rampaging barbarians dedicated to tearing down civilization. Which is why they got a radical reboot in 2nd Ed; the whole "tear down civilization" bit is limited to a few batshit crazy members, and most of the Lunars are dedicated to making a new civilization outside of the models of the Solar Deliberative and the Realm.
...Which is, in turn, on its way out due to an oversaturation of secret masters of Creation and the 2e history of the Lunars being written to make everyone seem like an asshole with no redeeming features at all, number one case in point being the presentation of the Unconquered Sun as a tyrannical maniac with regard to Solar Bond (though the lack of other, similar accounts in the manuals for Dragon-Blooded and Sidereals, and the origin stories of the Incarnae in Glories of the Most High point to a more benign origin). The aforementioned problems may be slow to motively anger the readers on account of the second edition lacking a massive, ugly Lunar Charm cloud with a perfect dodge based on Charisma.
Also, pretty much the entire first half of Manual of Exalted Power: The Infernals, due to a spectacular failure of communication. To quote Rand Brittain of rpg.net: "The word from those in the know is that Infernals left out the first four chapters. Not sure why that happened."
As it turned out, basically the whole of Infernals had to be taken out and shot, because Infernal charms were calibrated precisely to Exalted 2nd Ed's mechanics. When the writers overhauled the mechanics to 2.5... Infernals broke irreparably.
There is also a bit of disagreement over the existence of Sidereal Martial Arts, as described in the Scroll of the Monk. Some disbelieve them entirely, others use some, but revoke the blatantly game-breaking or badly written ones (like Quicksilver Hand of Dreams).
At one point in Compass of Celestial Directions: Malfeas, there's a piece of background that badly strains the "no resurrections or time travel" rule. The fans immediately took this down to the back paddock and shot it, and the writers later dug its grave.
In the end, the writers decided to Malfeas with 2e's nightmarish mechanics, because they'd spent several thousand dollars' worth of unpaid time trying to fix things, and still hadn't managed to patch all the big problems, even with 2.5. Instead, they decided to start over from scratch, with a new edition and a new system.
There are more than a few gamers that insist that West End Games never lost the Star Wars license.
Wizards of the Coast downgraded the Magic: The Gathering set "Homelands" to not-worth-the-cardboard-it's-printed-on status when it "completed" the Ice Age block with Coldsnap. Most fans had already demoted it to that status years earlier.
Of course, the printing of plane cards referring to the Homelands setting and creatures like "Barony Vampire" in the base set indicates that Wizards isn't quite done with Ulgrotha yet - they just wanted to get it the hell away from any other Magic settings.
Early in design for the Innistrad set, it was suggested that it could be a return to Ulgrotha. Lead designer Mark Rosewater said no, partly because he wanted to create a horror setting free from any baggage of an existing setting, but mostly because of this trope.
Yu-Gi-Oh! duelists would like to remind you that, except for a very few token cards, there were no such sets as Cyberdark Impact or the Gold Series, or deck types such as all incarnations of the Hero cards (Elemental, Destiny, and Evil Hero) or Neo-Spacians.
Don't forget the people who completely ignored the banlist.
There's a quiet chunk of players who refuse to acknowledge synchros, XYZ, deck limits, card restrictions and in extreme cases the existence of the extra deck in general.
A fair few fans of BattleTech have elected to ignore the Dark Age era, along with its attendant click-based game, and presume that the Inner Sphere is still rebuilding after the Word of Blake Jihad, another rather controversial event that a not insignificant chunk of the fanbase doesn't want to acknowledge. Not all fans agree on what is and isn't in keeping with the game's tone and bounds of believability. What most fans will agree on is that the novel Far Country has no place in the canon, and in a strange way, the line developers agree. While the devs won't outright RetconFar Country out of existence and still declare that as a BattleTech Expanded Universe novel it is canonical, not a single work since then comes within shouting distance of the idea of aliens existing in the Battletech universe. They'd rather just leave it in a cleaning cupboard and not think about it.