The canonicity of TaleSpin and Chip 'n Dale Rescue Rangers in relation to the wider Disney comic universe is unclear at best. The Crisis CrossoverLegend of the Chaos God seemed to show Talespin as taking place about fifty years before the "present-day" of both DuckTales and Chip 'n Dale Rescue Rangers (which in itself is not without its problem, as Rescue Rangers was previously implied to be a reboot of Chip and Dale in a universe stripped of Donald Duck and Co. entirely). But then a Disneyland stage play showed Don Karnage from TaleSpin and Fat Cat from Rescue Rangers cooperating on a heist in the present day, with no time travel in sight.
There are absurd numbers of conflicting versions of Atlantis in that universe, ranging anywhere from an ordinary Cretes-like island in Vicar's The Secret of Atlantis to a futuristic Magitek-based society in Casty's Atlantis Cycle. House of Mouse even suggests that Atlantis: The Lost Empire is canon to the comics (though obviously, the reverse is not true). Note a brave attempt at Fan Wank unifies most of this mess, as seen here, though it forces one to fudge around some elements here and there.
Donna Duck was initially introduced in the cartoon Don Donald as Donald Duck's girlfriend. The cartoon's ending seemed to show them breaking up, but Donna herself, aside from her name and appearance, looked identical to the then-not-created-yet Daisy Duck. Indeed, Daisy herself was soon established as Donald's steady girlfriend (and let's not go into how/when the two met, please). But the British Mickey Mouse comics kept using "Donna" as the name of Donald's usual girlfriend for several years. It became somewhat accepted that "Donna" was just an older name for Daisy, like "Dippy Dawg" for Goofy, and the two had always been one and the same. But that truce was not to last, as Al Taliaferro's comic strip showed Donna and Daisy meeting (seemingly for the first time), with Donna referred to as Donald's former girlfriend. Alright, fine. This became the norm as well, and was referenced in a couple of European stories too. But then one other Italian story showed Don Donald to not be canon at all, and, invoking a peculiar brand of Direct Line to the Author, showed that the cartoon was an in-universe comedy film in which Donald and Daisy starred as actors. To mess it all up even further, Don Rosa foolishly released Word of God (or Word of Dante depending on who you are) claiming that Donna was actually Daisy Duck's sister and the mother of recurring characters April, May and June. You may recall that Taliaferro's strips, the only preexisting source to establish that Donna and Daisy were separate entites, clearly showed they didn't know each other. (To add to the insanity, the Inducks database lists the British Donna Duck and Taliaferro's character as separate ones, for whatever reason.)
As if this was not confused enough, Don Donald was released on VHS several times, billed as Daisy's first appearance (once on a tape entitled Starring Donald and Daisy). Leonard Maltin notes Don Donald as Daisy's debut in his intro for the first Walt Disney Treasures Donald volume, but concludes that she does not "become the Daisy Duck we know and love" until later on.
Firstly, their (only — we'll get to that) DuckTales story arc, "Rightful Owners", was an ambitious attempt at Canon Welding tying the classic comics and DuckTales (1987) into a single continuity; the comic finally showed Donald returning from the navy, thus serving as a finale for the show. Alas and alack, they messed some of it up. Most glaringly:
The 'Golden Fleece' scene unconvincingly tried to mix the comic's backstory and the (completely different) cartoon, where the Dragon and the Fleece itself are in a state that fits the ending of the comic, but the Harpies guarding the two are the ones from the cartoon, who, on top of everything else, act as though the Ducks only visited once, so you can't just pretend the cartoon and comic Harpies swapped jobs or something.
The Golden Helmet is seen in Scrooge's collection of artifacts, and Donald and the nephews acts surprised at this, as (they say) they last saw the thing when they threw it into the sea, obviously calling back to the original Barks story. (What Happened to the Mouse? is involved here, since obviously how Scrooge got the Helmet was going to be addressed had the comics had a long run.) However, this ignores the Don Rosa sequel to this comic where the Helmet was fished up by Goodluck Gander, in full knowledge of Donald, before turning out to be worthless in the end. This can't be a case of Canon Discontinuity on Rosa's stories, either, because Don Rosa's comics are explicitly referenced elsewhere.
Moreover, Boom losing their licence (presumably due to the aforementioned royally messing up the continuity) meant they had to wrap up their gigantic Canon Welding in four issues flat to lead into the Dangerous CurrencyCrisis Crossover with Darkwing Duck. As a result, the dozens of villains gathered by an unseen force turned out to have been simply rounded up by Rockerduck… even though it makes no sense for some of them to be there since they don't have anything to do with the kind of job Rockerduck would need them to do…
Then said Crisis Crossover rolled round and lo, it messed up the continuity even further. Mrs Crackshell now knew about Fenton Crackshell being Gizmoduck's Secret Identity, even though she knew no such thing; whereas Darkwing Duck acts surprised to discover it, even though he'd already found out in the original TV series. Because clearly this wasn't bad enough, they then confused up the lore surrounding the Tronsplitter, where, now, the original "soul" of the divided person is sent to a Pocket Dimension even as the split halves retain individual consciousness. You'd think Darkwing Duck would have mentioned something like that when being put back togehter the first time around, but nope. And to confuse things even further, this is, somehow, the same pocket dimension that Morgana McCawber was sent to by Duckthullhu… for… no discernible reason, really.
Wait, we're not through yet! You see, Dangerous Currency was released illegally by Boom, as they'd actually already lost the licence by the time they got around to printing the sorry mess of a story arc. So Disney, being pretty pissed off by this, proceeded to declare Canon Discontinuity onto Dangerous Currency. Specifically onto Dangerous Currency. Rightful Owners's validity was not addressed, and likely won't be now that future DuckTales comics will presumably be in continuity with the 2017 reboot, leaving the old show's continuity behind. Not to mention the hints about Dangerous Currency that had been dropped in still-canon previous issues of the Darkwing Duck comic. The 2016 comics looked like they were going to address the issue, with a (hopefully better) remake of Dangerous Currency… but then that got cancelled, too, before it could contribute anything much.
Other
The 2000 AD strip Strontium Dog. The guest appearance in Judge Dredd revealed that Johnny Alpha's adventures took place in the future of the Dreddverse, even though that was hard to square with Strontium Dog continuity (basically, where did all the Mega Cities go?) But then it turned out that didn't even matter, because the strip was rebooted in 1999, with the explanation that the previous run, Dredd crossover and all, was just a legend, and this was the true story. Which didn't stop spin-off strip Durham Red sticking with the original version. And then John Wagner returned to the original continuity, making the reboot non-canon...
Prior to the Continuity Reboot, the book had this problem early on, particularly with trying to adapt Sonic Adventure and Sonic Adventure 2. With Sonic Adventure, the big problems were that, beforehand, the comic was running with the idea of Humans Are the Real Monsters, depicting them as Four-Fingered Hands types that were destructive and war-like even with exceptions like Nate Morgan. Sonic Adventure had normal and accepting humans, which clashed with this. There was also the fact that Station Square was nice and clear, compared to the rest of Mobius. It was explained that this was a hidden colony of humans who survived After the End.
Then, there's everything involving echidnas and Chaos' origin. Echidnas first - when Knuckles first appeared, he was still Last of His Kind. When his mini-series was launched, it revealed his dad was alive. His series expanded that to saying there was an entire city of echidnas still alive, along with a group who preferred technology and more of Knuckles' family! Enter Sonic Adventure and the Knuckles Clan! How does a group of Mayan-inspired echidnas fit in with the technologically-superior ones we see now? Oh, they're a group of echidnas that decided to forego tech and turn native. For Chaos, the games proclaimed that he was trapped inside the Master Emerald and freed by Dr. Eggman. However, in the comics, the Master Emerald was never created until about a year or so before the game came out and Mammoth Mogul was stuck in it. So, they stuck Chaos inside a black Emerald-like item, then had Eggman shatter the Master Emerald, freeing Mogul.
The last 2005 BIONICLE comic, Fractures, ended with the six Toa Hordika marching into the Coliseum to confront the villains, with a note informing the readers that the Cliffhanger will only be resolved in the movie released later that year. The movie of course contradicted the comic's last few pages — only five of the Toa Hordika broke into the Coliseum, not to defeat the bad guys but to free their leader Vakama, who's become evil due to Roodaka's persuasion. In the comic, Roodaka never even meets him, although his turning evil is foreshadowed. The Hordika are also accompanied by the legendary beast Keetongu, who's only talked about in the comics, but doesn't actually appear. Some of the 2004 comics also had smaller inconsistencies with that year's movie — for example, did Vakama learn how to use his launcher as a jetpack and Matau his blades as wings before or after traveling to Ko-Metru?
The stardate the story is set in places the main story in roughly 2289. However Star Trek IV: The Voyage Home was set in 2286. Not only has Gracie still not had her baby — despite a humpback whale having a gestation period of eleven months — but the entire plan by Kirk, Kor, and T'Cel relies on luring the creatures into an ambush after determining they were monitoring a particular spacelane for major celestial events. While all other encounters (Farragut being attacked by the Cloud Creature, Phoenix's engagement after Kirk destroyed the Planet Killer, and V'Ger's approach to Earth) occurred immediately following the inciting events, this would require the creatures to wait for three years. The handwave is made that Kirk and his comrades used back channels to keep traffic out of the area until he could put his plan in motion, however that still creates numerous problems.
Gillian Taylor claims she had to partly re-learn English in the 24th century since it changed so much in her time. Star Trek IV: The Voyage Home though (which preceded this) showed no problem with her speaking to Kirk or Spock, nor vice versa. The rest of the crew also had no issues while on Earth.
Rogue Trooper was a strip about a genetically-engineered Super-Soldier named Rogue who fights a one-man war on Nu Earth, accompanied by the digitised minds of three of his comrades in microchips attached to his helmet, gun, and backpack. Makes sense. At some point he met a woman of his race (for want of a better word) named Venus Bluegenes, who died. No problem. Later on, the series was given a brand new reboot, using Dave Gibbons' original vision, starring a new GI named Friday. So far so good. Then Venus got her own spinoff, but set in Friday's continuity. Uh, well, maybe she's an alternate version. Then Friday met Rogue and everything stopped making sense.
Vampirella has one almost as bad as Hawkman. She begins her origin as a Human Aliens vampire who comes from the planet Drakulon only to find the Earth is full of supernatural vampires. It's a cheesy fun juxtaposition of science fiction and fantasy you'd find in the 1970s. Then Harris comics retcons Vampirella's origins so she's actually the daughter of Lilith Brainwashed and Crazy into believing she's from the planet Drakulon. A remorseful Lilith raised her in the Garden of Eden to hunt monsters and her evil siblings. Lilith would then be retconned into a villain or a good guy who had villainous tendencies depending on the era. Oh and Drakulon would be revealed to be a place located inside Hell. It reaches its zenith in Dynamite Comics' 2011 book where Vampirella is revealed to have two mutually contradictory sets of memories about being a Human Aliens vampire and the daughter of Lilith. There's also ample evidence of both being true spread throughout the series with the opening stating she has a Shrouded in Myth origin. The 2016 comic has gone back to making her an alien with no mention of the other elements.
The first book of Blake and Mortimer, "The Secret Of The Swordfish", begins with what is hinted to be World War III, even if the date is not specifically givennote the U.N. is referenced and London is said to be "once again" in flames - later books, written by different authors, set this story as happening in 1946. The next book, "Mystery of the Great Pyramid", references events from the first book, setting it unambiguously some time afterwards. It ends with Olrik wandering off in the desert after having his memory wiped. In the third book of the series, "The Yellow "M"", the Big Bad recounts in a flashback how he encountered an amnesiac Olrik in the desert, then went back to London shortly before World War II began. So, to summarise, we have WWII, then WWIII, then Olrik gets lost in the desert, then he is found some time before WWII... It is no wonder that the later books by original author Jacobs slowly pushed "Secret of the Swordfish" into Canon Discontinuity.
The first series of DC Comics's Star Trek: The Next Generation comics had an odd set of dates. The first issue takes place on Stardate 41187.5, which puts it between "Encounter at Farpoint" and "The Naked Now", the first two-three episodes of the series. The second issue takes place at Stardate 42120.3, which still puts it before "The Naked Now". However, the third issue suddenly jumps ahead to Stardate 42125.7, which would put it between "The Child" and "Where Silence Has Lease", Season Two episodes that hadn't even been thought up of at that time and suddenly hits this trope as, by that time, Tasha Yar should be dead and Dr. Beverly Crusher should have been replaced by Dr. Pulaski. The final issue suddenly decides to go back in time to Stardate 41753.8, which puts it before "Conspiracy" but still after "Skin of Evil" and Tasha Yar's death, discounting the logistics of how the final issue can take place after the events of issues 3-5 yet be set before them.
The Scrameustache has a crossover album with another Franco-Belgian Comic, Les Petits Hommmes, clearly implying the two series are happening in the same world. However, both comics have their own separate take on the myth of Atlantis, and they are not reconcilable.
, though it forces one to fudge around some elements here and there.