In Bleach, Aizen seems to be strangely misinformed about his Arrancar followers, labeling Grimmjow's posse "gillians" when they had, in fact been adjucha before being turned.
Urahara likewise seems curiously ignorant with regards to the origins, goals, and membership of the Vizards, given the degree to which their backstories are intertwined with his own.
Also, several cliffhanger moments picked back up with a character repeating the final few lines of the past chapter/episode/commercial break, only different. One such example of a sentence that started "Shinigami and a..." was changed to "Human and a..." a week later. This one sentence sent the fan speculation wild in the intervening week, as the speculated ending "Shinigami and a... Hollow" would be much more explanatory, but also a Voodoo Sharknote It would explain Ichigo's powers, but it would also suggest his mom had some sort of Hollow lineage/power, while the "actual" sentence "Human and a... Shinigami" explains more or less nothing.
Blood War spoiler: Apparently, Ichigo's mother was a Quincy. This does give her ample opportunity to be attacked by Hollows, and might even have been planned in advance, given past revelations about Isshin and Ryuuken.
Numerous details introduced early in the series were quietly dropped after the Genre Shift to a more action-oriented series. Rukia claims that Shinigami kill Hollows from behind so that they won't see their human faces as they dissolve, but no Shinigami are ever seen doing that. A method of tracking people using things called Spirit Ribbons is also never seen again after the initial arc, with all of the characters tracking each other using only their spiritual power. In fact, the afterlife aspect of the series is often inconsequential, with various aspects of it (the reincarnation cycle, who hollows were before they changed into hollows, the possibility of Shinigami having once been humans themselves, and Hell) remaining unexplored in favor of battles between the various spiritual factions.
In the beginning of Fist of the North Star, it is implied that Kenshiro and Shin are the only successors of the Hokuto Shinken and Nanto Seiken martial art schools respectively. This is especially notable when Kenshiro reminds Shin that they must cooperate and help each other passed on their martial arts to future generations. After Shin's death, it is revealed that the Nanto Seiken style has exactly 108 schools as other practitioners of the style are gradually introduced and while Hokuto Shinken had a clearly established one successor rule, there were other students of the art besides Ken himself who were not chosen for the succession.
In Naruto the naming conventions and other things of stronger ninjutsu are a bit different in the beginning. In the Wave Country arc, stronger attacks took a ridiculous amount of hand seals, with the water dragon one (B-rank) taking 42. After that, even the strongest techniques never used more than ten. Also, in the first arc most attack names were proceeded with "Ninpou (ninja art/technique): (name of technique)", which was dropped later.
When Sasuke is with Suigetsu on his way to recruit Karin into their group, he speaks of her long-range chakra-sensing abilities as if it's something completely unique to her. Later, Killer Bee sees her sensing his location he refers to her as a "sensor-type", implying long-distance chakra-sensing is an ability other ninja can have, although probably a rare one (which is later confirmed when no less than three more of them show up two Story Arcs later, and an even later one has an entire division of an army made of them). In light of this, Sasuke's words come off as either misinformed or meaning her "unique power" was simply an individual and somewhat unusual version of it.
It was later retconned that her unique abilities are in reality a tremendous life force and Healing Factor since she is a member of the Uzumaki clan.
Naruto's own signature Kage Bunshin no Jutsu (Shadow Clone Technique) is an example—in the first story it gets treated as a dangerous technique and rare due to how much chakra it consumes. Later on this is said to apply to only the Mass Shadow Clone Technique (i.e. creating lots of clones at once) - the smaller-scale version is fairly common among Leaf ninja, and its high chakra cost merely makes it inefficient in most situations rather than directly endangering the user.
If you go back and reread the Chuunin Exam arc again, it's exceedingly obvious that Gaara was never meant to be a jinchuuriki- the concept of jinchuuriki didn't exist before the timeskip. He was simply an Evil Counterpart to Naruto, a boy with a monster inside him who succumbed to the darkness and became a killing machine. The most obvious evidence is the fact that Shukaku's powers and the form in which it manifests bear NO resemblance to any of the other jinchuuriki seen later in the series. Additionally, Shukaku was given its own backstory- far from being a "tailed beast", it Was Once a Man. (However, this has since been retconned as the citizens of Suna being unaware of Shukaku's true nature as a Tailed Beast and only assuming the Was Once a Man backstory to be the truth.)
Later subverted as we learn the real reason for Shukaku's odd backstory and this turns out to have been a minor Chekhov's Gun; The old monk was one of the Shukaku's previous jinchuriki, and he was treated as a monster. He was locked in a cell, given only bread and water and was treated with utter disdain. Refusing to call him his real name, instead calling him the Shukaku. This is why everyone thought that Shukaku wasn't a tailed beast.
The Byakugan is introduced as if it would be much more powerful and important than it ends up being. During the Chunin exam 3rd stage preliminaries, Kakashi states that the Sharingan was originally a mutation of the Byakugan, and the latter's ability of insight surpasses the former's; he then adds that if Sasuke and Neji were to fight, Sasuke would have zero chance of winning. This status quo falls apart as the plot progresses. We are gradually introduced to the game-breaking Mangekyo Sharingan, an evolution of the sharingan with a wide range of abilities that each far surpass anything the Byakugan could possibly do. Later, we also find out about the Rinnegan, which has ominous ties to the origin of ninjutsu and has its own range of game-breaking abilities; we then come full circle as we find out that it was, all along, an evolution of the Sharingan. By the end, the Sharingan and its evolutions are a top tier force to be reckoned with, tied intricately into the series' convoluted Myth Arc, while the Byakugan is the exact same kind-of-cool power with unrealized plot potential that it was during its introduction. To add insult to injury, ultimate villain Kaguya apparently has the Byakugan, but she goes down in short order without showcasing a single Byakugan ability we haven't seen before, and due to the series being Cut Short we will probably never learn why she even had it in the first place.
In Pokémon Special an earlier chapter has Red capturing a Gyarados that already belong to another trainer (Misty). However, at a later point, Blue/Green says that, as is explicitly shown in most other parts of the franchise, catching a Pokémon some else has already caught is impossible.
The Pokémon anime also seems inconsistent at how many Pokémon a trainer could carry. An early episode features a trainer who carries plenty of Poké Balls at the time, shortly afterwards we're told they're only allowed to carry six. What happens to the seventh' has also changed. Ash's Krabby simply disappears soon after he caught it and gets sent to Professor Oak. But when he catches Sewaddle in Unova the Poké Ball simply shrinks down and becomes unusable until Ash sends one of his other Pokémon away.
Hiei initially points out that he and Yukina are half-siblings with different mothers. In the Three Kings Saga, it's revealed that the two have the same mother, were born at the same time, and Hiei was conceived by a man, while Yukina was conceived asexually.
At one point, in his introduction, Kurama says he's 300 years old. Later he claims to be a thousand.
A purely aesthetic one, but still noteworthy mistake in One Piece. Robin, who is 28 at her introduction, got her first bounty when she was 8, and when some Marines recognize her, we see the bounty poster with a picture of her 8-year-old self in an Imagine Spot. On the picture, she has almost the exact same face as her adult self (though her nose is smaller and her hair shorter). The only thing that really gives her off as a kid is that she has the head-to-body-proportions of a young child. 200 chapters later, we get to see a long flashback with 8-year-old Robin. Now she is suddenly drawn with a more childlike and cuter face (bigger, rounder eyes and a different nose) which doesn't really look like her bounty poster picture. Later in the flashback, her bounty poster is issued and it does have her more mature-looking face on the photography, though outside of the poster she still has her cute child face. One would almost think the Marines traveled to the future, took a picture of her 28-year-old face and photoshopped it on her 8-year-old body...
Some of the exposition about the setting at the start of the series seems to be at odds with how things are portrayed later. The Grand Line is described as being hell-on-earth. While it is dangerous, it also seems to contain the majority of the world's population, and doesn't come off as the pirate's graveyard characters usually described it as. When the second half of the Grand Line, the New World, is introduced, it's described pretty similarly to how the whole Grand Line was portrayed before the characters actually got there. Several characters also treat Devil Fruits as nothing more than myths, but the vast majority of the most famous people in the world have eaten a Devil Fruit, which makes it hard to believe that their existence would be in dispute.
In the pre-CrisisSuperman comics, it's explicitly stated that Superman is the last son of Krypton. This is fine for a while... until Supergirl, Krypto the Superdog, and more start showing up. Someone once commented that Jor-El and Lara seem to have been the only people killed in the destruction of Krypton. That someone clearly never read the Superboy story that revealed they hadn't been, either. (And yes, if Superboy learnt this, then Superman should have known it all along.)
Hell, at least half of Superman's powers are the result of Continuity Drift and Power Creep, Power Seep. Originally he could lift a car over his head, outrun an express train, leap 1/8 of a mile, had telescopic vision and super-hearing, and "nothing but a bursting shell could pierce his skin". Later comics and cartoons gave him a long list of other/greater powers. The ones that stuck include the power to fly, the strength to lift ocean liners and move colossal space cruisers with his bare hands, enough speed to compete with the Flash in a foot race and (sometimes) make inter-stellar flights, super-breath/freeze-breath, invulnerability to anything other than magic or kryptonite, and expanded his vision powers to include x-ray vision, heat vision, microscopic vision, and the ability to see across the entire electromagnetic spectrum.
Even the origin of his superpowers changed within the years — as this page illustrates, Krypton was originally populated by Human Aliens that are more athletically evolved than the Earth humans, but eventually "The Complete Story of Superman's Life" was published, establishing that a Kryptonian can only gain super abilities on Earth, due to being born on a planet with heavy gravity and a red sun.
For his early appearances in Garfield, Nermal was owned by Jon's mother. Now he just wanders in whenever needed.
Similarly, Odie used to belong to Jon's friend Lyman. After Lyman vanished, Odie became Jon's pet. Some fans believe digging up Jon's back yard could be... enlightening. Word of God on the issue is "you don't want to look in Jon's basement".
One of the stories in Garfield: His Nine Lives is an alternate history of Odie being bought by Jon as a companion for Garfield.
In Strontium Dog, the term 'strontium dog' was originally an insult, and in an early strip, Johnny forced his client to pay him a higher fee after they refer to him as such. After a year or two, nobody seemed to care — Johnny referred to himself as a strontium dog, as well as his fellow bounty hunters.
Marvel'sNamor has the following as his current powers: Hulk-level super strength, flight, amphibious physiology, and a bad temper. When he was introduced, and well into the sixties, he could also talk to fish and mimic the abilities of any undersea creature, including puffer fish. No one really talks about these powers, but it's possible he only doesn't use them because it would make him look stupid.
In Judge Dredd, Judges seem to have originally been portrayed as an elite unit within the regular police force, and some early strips feature non-Judge cops as redshirts. Nowadays, the entire police force is composed of Judges.
The first published Judge Dredd comic describes Dredd as operating in New York City and as having been elected to his post. Later, New York was revised to just part of Mega City One, and Judges were presented as having passed through an intense years-long training program before being graduated to duty with no election necessary. It could be a case of Fridge Brilliance — they ran out of redshirt regular cops and/or realized that they can't do the job, so you don't see them any more.
If you're a Fables fan you'll notice this happen often. Legends in Exile has a lot of differences to the later books. The community is suggested to be much larger, Beauty and Beast requiring a carriage to attend the annual Remembrance Day ball, yet by March of the Wooden Soldiers we can see that Fabletown is just a single, small street with a few hundred residents, most of whom live in the woodland building.
Green Lantern ran into this with the comic's first issue, which depicted Hal Jordan's predecessor Abin Sur dying after crashing his spaceship on Earth. It made perfect sense to readers at the time (everyone knows that aliens get around in spaceships, after all), but later issues would establish that Green Lantern rings give their bearers the ability to breathe in space and fly at near-lightspeed, making spaceships unnecessary in the Green Lantern Corps. Various retcons and re-imaginings would later attempt to explain away the discrepancy by crafting reasons for Abin Sur to use a spaceship in his final mission, thus keeping the origin story intact.
In the pre-Crisis story "Earth's First Green Lantern," Abin Sur used a spaceship in a ploy to trap a parasitic alien by convincing it that his ring had run out of power (since, of course, a Green Lantern would only resort to using a spaceship if he couldn't use his ring).
In Alan Moore's post-Crisis story "Tygers," he used a spaceship out of fear of a prophecy foretelling that his ring would fail him at a crucial moment, leading to his death. The prophecy ended up causing his death because it led him to lose faith in his own power ring (which, of course, requires willpower to work).
In Geoff Johns' post-Infinite Crisis retelling of his origin story, "Secret Origin," Abin Sur lost faith in his ring because of a prophecy foretelling that Parallax's influence on the Corps' central power battery would corrupt him, leading him to rely on a spaceship for his interplanetary voyages. He also needed the spaceship's holding cell to transport Atrocitus, an enemy of the Corps, back to his crucifix at the prison planet of Ysmault.
In the Green Lantern film adaptation, the "spaceship" is changed to an escape pod, which a mortally wounded Abin Sur uses uses to escape Oa following a tumultuous battle that cripples his ability to use his ring.
A few issues after the original clone story was published, there was a story that revealed that the Spider-Man clone (later named Ben Reily) was a partner of the Jackal (the initial villain mastermind behind the Clone Saga) who had been turned into an exact clone. This revelation was brought on by the High Evolutionary, a man who was on the level of Reed Richards or Doctor Doom. When Marvel Comics brought the clone back, they had a quick throwaway line that the High Evolutionary was jealous and lied. This means that the Jackal, a B-list villain and lowly university professor, had somehow managed to one-up a man who had made himself as powerful as Galactus.
Miles Warren the Jackal was eventually revealed to have been the High Evolutionary's assistant at some point.
Many new clones were introduced as being made before Ben Reilly, making him much less special.
Readers were subjected to this within the saga itself. The story also introduced a mysterious villain named Judas Traveler who was a mystic that had a wide variety of powers including Time Travel. The writers had no idea who this villain was, nor did they know what to do with him. It was eventually hand-waved that he was a mutant with the ability to cast illusions which set up many plot holes since the man was nearly omniscient.
The story was also responsible for bringing back Norman Osborn from the dead. Not only did this slap a huge Retcon on a story that was written 20 years earlier but it negated the actions of the Jackal throughout the Saga.
Very early in Preacher, Cassidy survives being shot by the Saint of Killers. A vampire surviving being shot is no big deal, but we later learned that the Saint's guns were forged by Satan himself from the Angel of Death's sword and made so that they will never miss, never run out of ammo, and always kill whatever they hit. The first thing the Saint does with them is shoot the Devil in the face, and at the very end of the series he kills every Angel in Heaven and God himself with those guns. Garth Ennis later admitted that he didn't realize where he would eventually go with the Saint, and we should just try not to think too hard about that early encounter or why Cassidy survived.
Fridge Brilliance: Cassidy wasn't killed by the Saint of Killer's guns because he was already dead.
Disney comics aren’t heavy on continuity to begin with, so it’s no surprise that they sometimes fall prey to this trope. When Scrooge McDuck first appeared it was not explained where he got his money, but he was implied to have been born rich — e.g., in “The Old Castle’s Secret”, his second appearance, where he refers to his own wealth as “the McDuck fortune” (suggesting that it is in fact the family fortune), and owns a huge ancestral castle. A few years later, in “The Magic Hourglass”, it’s stated that he was not born wealthy, but became so through the power of the titular amulet. Finally, when Scrooge was given his own spinoff title (and was no longer just a supporting character in the Donald Duck series) it became necessary to turn him into a more sympathetic, and even heroic, character; it was at this time that his current backstory was established: that he was born into poverty but rose to riches purely through his own grit and ingenuity (by being “smarter than the smarties and tougher than the toughies”) — the quintessential Self-Made Man. This is the foundation on which all of his later characterization is built.
Ice Age was set during a real ice age with humans. The sequels have more anthropomorphized animals, dinosaurs, pirate monkeys, Scrat causing continental drift twice - and no humans. However, as humans were extremely rare when Ice Age takes place it's possible they just never crossed paths.
Star Wars: The prequel trilogy was written many years after the original trilogy. Some implications in the original trilogy don't seem to mesh very well with what the prequel trilogy reveals — to say nothing of continuity hiccups with the Star Wars Expanded Universe (which was divided into a lower class of Canon. The possible explanations for these rifts vary in how far-fetched they are.
When watching the original Star Wars trilogy, one gets the impression that the Empire has existed for a long time. The prequel trilogy, however, shows that it's only nineteen years old. For example:
Admiral Motti dismisses the Jedi Order as an "ancient religion" and Han Solo sees The Force as superstition, suggesting that they never even saw a Jedi firsthand in their lives. However, 19 years ago they were a major force in the center of the Republic. Of course, you have to remember that Han is from Corellia, a world that tended to remain aloof from what was happening elsewhere in the galaxy; he spent practically all of his formative years on the fringes of galactic society (except in his late teens, when he briefly stayed on Coruscant with his live-in girlfriend); and while he was taught about the Force by the female Wookiee who raised him when he was a child, she only ever called it "the life power" in the Wookiee language, and Han never seriously believed her.
Tarkin announces the dissolution of the Senate as having swept away the "last remnants of the Old Republic", implying that the Senate had long been a powerless organ of a long-defunct government.
Also related is Obi-Wan's line in the original movie about the Jedi serving the Republic for over a thousand generations before the dark times of the Empire. However, in Attack of the Clones, it's stated that the Republic was formed a thousand years ago. The continuity wizards at Lucasfilm fixed this by stating that the Republic was merely restructured around that time.
When Vader tells Tarkin that Obi-Wan is aboard the Death Star, Tarkin says, "Obi-Wan Kenobi? Surely he must be dead by now." Vader replies, "Don't underestimate The Force." This implies that if Kenobi weren't a Jedi, he likely would have died of old age by then. The prequels set Kenobi as no older than his 60s during A New Hope, hardly an improbable age.
Obi-Wan says, in Return of the Jedi, "When I first met him, your father was already a great pilot, but I was amazed at how strongly the Force was with him." It's technically accurate, but surely he would mention Anakin was already a great pilot at the age of nine? But that detail didn't exist at the time. Also, in The Phantom Menace, Anakin had more interaction between Qbi-Wan's master Qui-Gon, who became almost a father figure and was the true impetus behind Anakin learning about the Force. Lucas originally had Obi-Wan take Qui-Gon's role in the final film but decided to age him down and introduce Qui-Gon to show a proper Master-padawan duo.
Obi-Wan says in the same instance in Return of the Jedi that his chief failing was thinking he could train Anakin as well as Yoda. This is nowhere apparent in the prequels and the one pushing for Anakin being trained is Qui-Gon. Obi-Wan merely trains Anakin as a final favor to him.
Obi-Wan addresses Vader as "Darth", having earlier referred to him as "A young Jedi named Darth Vader", implying that "Darth" is his first name. The prequels and Expanded Universe show that it's actually a title, akin to Vader calling Obi-Wan "General" or "Master". In retrospect, the scene works very well if we declare that Obi-Wan is making a point out of refusing to call Vader by his name. But when the first movie was written, "Darth" was really just Vader's first name. (And he really did murder Luke's father, who only became Vader himself for The Empire Strikes Back.)
Ben also says in The Empire Strikes Back that Yoda was the Jedi Master who instructed him. Yet in Episode I, he's the padawan of Qui-Gon, not Yoda. In Episode II, Yoda is shown teaching a large class of younglings, implying that Yoda gives some training to many or all Jedi, but it's still not appropriate to say that Yoda was the Jedi Master who trained Kenobi.
In A New Hope, Obi-Wan makes it sound like Anakin Skywalker and Owen Lars had a long history together, saying things like "[Owen] didn't hold with your father's ideals" and "He thought [Anakin] should have stayed here and not gotten involved." Then in Attack of the Clones, we learn that the two aren't even blood relatives, and they only met each other once. Briefly, at that. They were originally intended to have been brothers, but this was changed (obviously).
In The Empire Strikes Back Obi-Wan's ghost thinks Luke is the Jedi's last hope, but Yoda notes "there is another"... who was of course revealed in Return of the Jedi to be Leia who was Luke's sister all along. But Obi-Wan does not seem to be aware that Luke even has a sister in Empire. This is because Leia was not Luke's sister when Empire was filmed, and only became so when Return was being written. Revenge of the Sith complicates things further by having Obi-Wan being present at Luke and Leia's births, even delivering them himself to their respective foster families.
The X-Men film series is rather infamous for this.
Dr. Hank McCoy makes his first appearance in a background cameo in X2: X-Men United, where he's a human-looking scientist being interviewed on a news program. When he appears in X-Men: The Last Stand, though, he's a politician with a spot in the United States Presidential Cabinet, and he appears in his classic blue-furred simian mutant form. But then the prequelX-Men: First Class, which reveals that he was one of Professor Xavier's original X-Men, shows that he's had blue fur since his early 20's, when one of his experiments went awry and accelerated his mutation.
In an Author's Saving Throw, X-Men: Days of Future Past reveals that Hank developed a serum that let him pass for human for short periods. It also clarifies the true nature of his close relationship with Charles Xavier, establishing that he was the only one of Xavier's original students that stayed behind when Xavier shut the school down during the Vietnam War.
A flashback at the beginning of X-Men: The Last Stand (which likely takes place in the late 1970's or early 1980's) shows Professor Xavier walking upright, and clearly still allies with Erik Lehnsherr. X-Men: First Class later reveals that Lehnsherr was responsible for paralyzing Xavier in 1962, and that their friendship ended immediately after.
Dr. Moira MacTaggert is first introduced in a brief cameo in X-Men: The Last Stand, where she's a British scientist who has apparently been friendly with Charles Xavier for years. But in X-Men: First Class, which takes place about 40 years before the rest of the series, she's an American CIA agent who has her memories of Xavier erased at the end of the movie.
When Sabretooth first meets Wolverine in X-Men, he never gives any indication that he knows who Wolverine is, even though he spends more time with him than with any of the X-Men. X-Men Origins: Wolverine later reveals that, not only do the two have an extensive history together (going back to the mid-1800's), they're actually half-brothers.
X-Men states that Magneto built his psychic-proof helmet around the time that Senator Kelly's Mutant Registration Act led him to ramp up the Brotherhood's terrorist campaign, since he knew that Xavier was tracking him. X-Men: First Class establishes that he's had his helmet since the 1960's, and that he originally stole it from Sebastian Shaw.
X-Men Origins: Wolverine features a brief appearance by Kayla Silver Fox's sister: a blonde-haired woman who's clearly intended to be Emma Frost (she has Emma's ability to turn her body into organic diamond, and is listed as "Emma" in the final credits). X-Men: First Class later explicitly introduces Emma Frost as a major character—who's around the same age as the character in Origins (even though the two films take place 15 years apart), has psychic powers that were never mentioned in Origins, and never gives any indication that she's related to Kayla Silver Fox.
In a possible case of Aborted Arc, X-Men: The Last Stand introduces Bolivar Trask in a small supporting role as the United States Secretary of Defense, but never gives him a major role in the story. He later reappears in X-Men: Days of Future Past as a major antagonist... where he's gone from a tall, middle-aged African-American military officer to a Caucasian dwarf scientist who was assassinated by Mystique in the 1970's.
Despite both being major characters with top billing, Professor Xavier and Mystique never seem to directly interact with each other in the original trilogy, and they never give any indication that they have a history... which is odd, since X-Men: First Class reveals that Mystique is Xavier's adopted sister, and that Xavier has known her even longer than he's known Erik Lehnsherr.
The first Redwall book kind of implies that there are humans around somewhere. It suggests the standard rules for talking animals (they just don't do it in front of people except for maybe one kid who has magical adventures with them, and let's ignore the implications as far as livestock are concerned), but this all goes away from the second book on. It is also implied that the humans are much larger and may not understand them.
The kitchens moved. Rowling intentionally wrote a bit in the first book saying how the layout of Hogwarts is constantly changing specifically to cover for this sort of thing.
The points are worth a lot more in the first Harry Potter book — Harry and company are mortified at the prospect of losing 50, let alone 150 points, but in a later book, Snape docks 50 points with only a passing mention. Steve Kloves (or Chris Columbus) tried to mitigate the point thing in the first movie. At the end of the first Potions lesson (the part left on the cutting room floor), Snape takes five points from Gryffindor whereas he only took one point in the corresponding scene from the book. (By the later books, taking five points had become the standard response to a minor infraction.)
In the first book, Hagrid describes the deaths of Lily and James as if they hadn't been actively against Voldemort already, and it was a mystery why he would even be bothered to kill them if the opportunity came up. In the third book, Fudge, telling the story of how Voldemort found them, mentions that it was "well-known" Voldemort had been seeking the Potters at the time, with Hagrid right there, and by the fifth, we learn that they served alongside Hagrid in the eponymous Order of the Phoenix the first time around. The effect is that in that first scene with Harry, Hagrid lied... a lot. The movie corrected this also, taking out the questioning of why Voldemort went after Harry's parents and having Hagrid simply say "your parents fought against him, but nobody lived once he decided to kill 'em."
In Goblet of Fire, the Death Eaters who tortured Neville Longbottom's parents into insanity are charged with having assaulted "an auror and his wife," which certainly implies that Neville's mother was not herself an auror. By the next book, however, Rowling had apparently decided that both of Neville's parents should have been aurors, making the phrasing of the charges in the previous volume extremely difficult to justify without positing a degree of sexism not otherwise evidenced in Rowling's wizarding world. (The most common explanation is that Alice was either still on maternity leave, or had quit to raise Neville, but still.)
In later books, you need only to say "Riddikulus" to beat a boggart. The whole "make it funny" part is abandoned after the third book.
Characters in the books have a tendency to refer to things in vague terms early in the series, after which they are only ever referred to by name. For instance, "the Azkaban guards" are mentioned several times in Chamber of Secrets, but never actually called "Dementors" until Prisoner of Azkaban. Similarly, the Wizard police are briefly called "hit-Wizards" in Prisoner of Azkaban before the term "Auror" is introduced in Goblet of Fire, and Voldemort's followers are never referred to as "Death Eaters" until Goblet of Fire introduces the term.
Discworld: In the words of Pratchett, there is no Continuity Drift. There may, however, be "alternate pasts". In other words, A Wizard Did It, probably by accident while trying to do something else.
And then the history monks, also known as the Men in Saffron, had to come by and try to sort it out as best they could. The classic "bug" is that the two major playhouses in Ankh-Morpork are the grand Victorian-era Ankh-Morpork Opera House from Maskerade and the shabby Elizabethan-era theater The Dysk from Wyrd Sisters, an obvious case of Anachronism Stew, especially since the Dysk was built in WS "a new type of building", and the Opera House has a history stretching back decades.
The Colour of Magic has references to the "other lords of the Circle Sea", and implies that Ankh-Morpork is simply the biggest and most crime ridden of many dangerous city states in the region. Later books show that the other 'cities' are peaceful, rural backwaters. The same book implies Ankh and Morpork were separate cities, a point that is never restated.
In the early Discworld books, Lord Vetinari comes off as an overweight Smug Snake, but in latter books, he morphs into the thin, perpetually-gaunt master-manipulator we know and love. Fans have attempted to explain this away by stating that it was a different Patrician of Ankh-Morpork, but Word of God has stated that this is not the case.
Same goes for Granny Weatherwax. In Equal Rites, her constant accomplice NannyOgg is nowhere to be found, she only wears her pointy hat when necessary, and she actually lets someone interrupt her without reprisal. It took a couple of books before she metamorphosed into the walking Crowning Moment Of Awesome she's known to be.
Equal Rites mentions the existence of Magicians (essentially failed students who are reduced to being lab assistants to proper Wizards) and Thaumaturgists (untrained dogs bodies who go and fetch dangerous spell components such as "the semen of a live tiger"). Neither are ever heard of again despite several books focusing pretty heavily on the Wizards.
Not completely true, in one of the Wizard Novels, Archchancellor Ridcully is referred to as a Magician and takes great offence at the comment.
A minor example: Nanny Ogg's Cookbook (1999) has a bit in the courtship section about sending coded messages by the positioning of stamps on a love letter. Nanny views this as a bit old-fashioned, from the days when "a girl wasn't expected to have any private correspondence until she was thirty-five." In Going Postal (2004), Moist von Lipwig invents the postage stamp...
Possibly Nanny was referring to how the stamping of a letter was oriented, rather than to stick-on paper stamps. Going Postal did show that old-time letter carriers had to rubber-stamp a letter to prove that its delivery had been paid for.
In a few early books it was a plot point that dwarfs age much slower than humans, to the point that by dwarf standards Nanny Ogg was barely the equivalent to a teenager and they don't even hit puberty until 50. In recent books they age at the same rate as humans and interspecies couples are said to have grown up together.
In the original version of book I, Roland discovers that the Man in Black he's been chasing isn't Marten but Walter. Later books in the series indicate that Marten, Walter, Flagg, and so on are the same adversary Roland's been chasing all this time, not just symbolically as "the Man in Black" but literally the same person. This is made explicit in the revised version of book I.
In book II, Eddie Dean is from Co-Op City, The Bronx, in 1983. From book III onward, he's from Co-Op City, Brooklyn, in 1987. This would be a simple gaffe, if not for the fact that it becomes a plot point that Co-Op City really is in the Bronx and Eddie's Co-Op City in Brooklyn is a sign that his world isn't the "real world".
There are tons of minor changes as well. For example, it seems like Roland's motivation for going to the Dark Tower changes every book as does the function of the Tower itself. Hell, Roland attributes the multiverse's imminent collapse on the Tower itself at the end of book IV. It's not until the last three that everything finally solidifies, probably due to King finally deciding what the Tower is and does.
King can't seem to make up his mind exactly how old Eddie and Susannah are. In one book, Eddie is twenty-three; in the next, he's "nearly ten years older" than Jake, who is consistently said to be eleven. This might be related to the aforementioned confusion over what year Eddie left his world. And in the third book, it's mentioned that Susannah is three years older than Eddie, while the second book implies that the age gap is much greater.
In the original version of book one, the Final Boss is referred to (in a very sinister manner) as The Beast. Turns out they meant the Crimson King all along, and he's not very tough.
The most obvious bit of Continuity Drift in The General series is the way Lady Suzette's eye color and the number of generations her family have been patricians vary from book to book.
Pick any two Oz books by L. Frank Baum and then work out a coherent history of that country and its populace.
This is lampshaded in Wicked, where Elphaba and Boq are searching through documents in their school's library trying to piece together the origins of Oz, and everything they find is confusing and contradicting.
It's not even just the history, it happens within the books. The Shaggy Man meets Polychrome for the first time twice, merely because Baum forgot he had introduced them in the same book.
Quite an infamous one among fans is that one of its shape-shifting heroes uses the telepathic communication they speak with while in animal form when he's in his normal human form. Every book afterwards features "thought speak" as only being functional when they're in bodies other than their own. K. A. Applegate (the author) herself has flat-out admitted that it was a mistake. The fan nickname for the incident and others is KASU, an acronym for "Katherine Applegate Screws Up/Screw-Ups". An extensive list can be found here.
There are also minor ones, such as the Yeerk naming system. At first, not just Visser but all names are treated as ranks, with at least three "Iniss [some number here]" people, with the You Have Failed Me victim among them serving as a reminder to The Dragon Iniss 226/Chapman that even "an Iniss of the third century" is expendable. A later Yeerk had had his number lowered as part of an advance in rank. After these early examples, no two non-Visser/Sub-Visser Yeerks will ever have the same name, or have attention called to their designation. Vissers' names before they were Vissers are considered their "real names" and are never "[Word here] 1."
We get bits and pieces of the Ellimist's backstory throughout the series... then the Ellimist Chronicles comes along, ignoring all of those bits. However, Marco mentions more and more leading up to it that "we don't know if he's one guy or part of a group." (When we first met him, he explicitly calls the Ellimists a group more than once. Some time after the last time, Marco decides it's a question for some reason. Then it turns out he's one guy — whose story has little in common with the hints given in the series proper.)
Related to the first KASU (a term KA actually uses sometimes!) is Ax's use of thoughtspeak in human form. At first, he mentions that as a human he must now use human speech. Eventually, though, he begins using thought speak in human form to talk privately with the other Animorphs. As human form is a morph for him, he still has it there. Apparently, he just... never thought to try it for over 30 books? Ax does obsess annoyingly over making mouth-sounds for fun, but telepathy would still have been useful in many situations.
Also, early on, thought-speak could send imagery and feelings as well as just words. This goes away fairly soon, though, and another alien race with its own version of thoughtspeak that worked exclusively on images and feelings eventually cropped up.
Whether "War Prince" is the rank after "Prince" or simply the full title and used with it interchangeably changes back and forth.
Crayak is a "he" until his very last appearance, then becoming an "it."
If you want to get really picky, when Visser isn't used as part of someone's name, is it capitalized or not? Visser Three is "the Visser" for a very long time, then becomes "the visser."
Early books seem to imply that the Yeerk homeworld is part of the Yeerk Empire—Visser One was apparently stationed there before visiting Earth in book 5, and the future Visser Three tries to use the Time Matrix to escape there in The Andalite Chronicles. However, The Hork-Bajir Chronicles states that the Andalites blockaded the planet soon after the war started, and the Yeerks still on that planet have no contact with the Empire; neither visser would even be old enough to have been born there. But why would Visser Three try to flee to a planet where his enemies are in control? Even with an Andalite body that seems like a pretty big risk to yourself and your new, incredibly-valuable super-weapon.
Early books seem to imply that the Yeerks had conquered numerous species; the Yeerk controlling Jake, for example, lists a couple random ones to imply how mighty the Empire is. Later books, however, never bring up any (totally) conquered species other than the Hork-Bajir, Taxxons and Gedds.
Kir Buluchyov's Alice, Girl from the Future series was notorious for this. Most notably, Krys (the Rat) a recurring villain, went from being a spider-like alien who changed shapes thanks to a holographic projector to a humanoid alien who changed shapes without explanation to a rat-like alien who changed shapes thanks to special pills. As Buluchyov himself admitted in an interview late in life, this was due to the fact that he didn't like to re-read his books.
J. R. R. Tolkien's The Hobbit is a prime example — it was rewritten at least three times to fit in with the wider Middle-earth mythology (e.g., in the first draft, Bilbo mentions the possibility of going to China). Even then, some incongruous details remain, like a talking purse, mountain giants playing catch with boulders, and magical boots that fasten themselves (invented by Gandalf). Tolkien said the earlier account of Bilbo getting the One Ring was a lie. The later and truer account was later written down after Gandalf questioned Bilbo about the ring.
His son, Christopher Tolkien, wrote in the preface to The Silmarillion that he had a devil of a time editing his father's as-yet unfinished material into something internally consistent, because this was so bad. But then again, it was unfinished, largely because J.R.R. kept going going back to the beginning to revise it.
The James Bond novels suffered from this. It's pretty much impossible to reconcile Bond's history as given in Casino Royale with his obituary in You Only Live Twice, unless the British secret service was in the habit of sending teenaged schoolboys out to conduct elaborate coups against the Bulgarians at the gaming tables of Europe. The Young Bond series of juvenile novels have done an excellent job at explaining away some of the inconsistencies (such as making his first car a gift from a dying uncle he received while still a teenager).
In the Vorkosigan Saga, in Warrior's Apprentice, it says that Vorhalas' sons were on the wrong side of Vordarian's Pretendership, whereas in Barrayar one is angry because the other was executed for dueling.
The angry surviving brother is strongly implied (maybe outright stated?) to have had Vordarian's backing in his assassination attempts, which Miles elsewhere refers to as part of the war. The duellist's fate might be pure drift, or might not: a lot of Apprentice is driven by Miles' parents' generation obfuscating some of the ugly details of that time period. It's quite possible Aral told Miles "he was killed in the civil war" in lieu of "he was executed for getting drunk and murdering his friend". (And also, much of the first part of Barrayar was apparently written before Apprentice.)
Alan Dean Foster's Humanx Commonwealth series started off the character of Flinx as a partially telepathic young thief, with the implication that his powers, though unusual, are not particularly terrifying and bizarre. The two mentor figures, Bran Tse-Mallory and Truzenzuzex, even comment among themselves that the boy is "a partial telepath", but apparently don't care enough to research the matter further. In later novels that expand Flinx's origin story, it's revealed that he's an empath, not a telepath, and was created as such by a universally reviled group of Evilutionary Biologists, so they really ought to have been more curious. Also, Flinx's age given in Bloodhype conflicts with the universal timeline Foster later established, the description of his ship is vastly different (to the point where Foster retconned it to be able to camouflage and reconfigure itself at will), and his pet minidrag is male, rather than the female it was established canonically to be in the chronologically earlier The End of the Matter.
Older than Television: For continuity drift within a single book try Kenneth Grahame's The Wind in the Willows. The relation between the anthropomorphic animals and humans changes between chapters. Initially the two groups are entirely separate, with the animals mostly ignorant of humans and their culture. Then Toad turns up, with his house, his ability to buy and drive cars, and his subjection to the criminal justice system — nobody notes his amphibian nature.
At first, battles were a lot more common and weren't treated nearly as seriously as they are in later books. In later stories, an border skirmish is a big deal and cause for concern about Clan wars, where in the early books it was the standard response to finding a trespasser: fight first, ask questions later. ShadowClan driving WindClan out in the first book was taken seriously, but if that happened in later books it would have been an instant Moral Event Horizon rather than the other Clans just raising a slight protest over the aggressiveness of the action.
A more minor example: The first book states that each apprentice must visit the Moonstone before becoming a warrior: they travel there with the leader when he or she decides to speak with StarClan. While we don't actually see it happen for the rest of the first series, it still gets mentioned occasionally. It's totally forgotten in the second series, and after it was pointed out by fans, the authors later Lampshaded it by having Leafpool say "We seem to have left that tradition behind in our old home." In the prequel Super Editions that take place before the first series, they do have the "each apprentice must visit the Moonstone" requirement again, but oddly enough it's the apprentices themselves, rather than the leader, that receives the visions from their ancestors at the Moonstone.
Empire of the Ants by Bernard Werber started out as a story among ants communicating with each other, where Humans Are Cthulhu. 327, a male ant, witnesses dozens of ants being killed at the same time by an unknown enemy, and asks other ants about it. A yellow ant tells him that he once saw several ants being killed like this, while crashed by a pinecone, and is described as "laughing" as this is "yellow ant humor". In the sequel books (Day of the Ants and Revolution of the Ants), though, the ants are described as not knowing what humor is and the humans have to describe it and teach them.
In Tom Holt's first J.W. Wells & Co. novel, using the eponymous Portable Door for more than an hour is incredibly draining, with potential risk to the user's life. By May Contain Traces of Magic, a character has pretty much relocated to his past (our present) using said Door, and isn't even remotely drained.
In the first few Honor Harrington novels, Harrington is described as winning in hand-to-hand combat due to her practice in martial arts and coming from a heavy-gravity world, while her deadly accuracy in a duel is due to single-minded relentless practice at a range. Later books and short stories in the series reveal that she's come from a family that's had some pretty extensive genetic engineering, giving her enhanced physical abilities that would have played a role.
Constance's eye colour in The Book Of The Dead changes from violet to blue to "dark" over the course of the novel.
In the first quartet of books in the setting, The Song of the Lioness, there are two kinds of magic. The Gift allows for things like starting fires, healing, and all the other active spells you can think of. The Sight is a passive magic ability allowing the practitioner magical insight into things they see. One character says that the Gift acts as a shield against those with the Sight. Three miniseries later, another character has the Sight so strongly she can see a great many things about people with the Gift.
Wild magic, introduced in the second quartet, allows for a different kind of magic than the normal Gift — the ability to talk to animals and eventually shapeshift. Hand waved by being subtle enough in most practitioners to be commonly disregarded as folk tale fodder.
Specific to the Provost's Dog trilogy, Beka's Psychopomp Gift. In Terrier, it's something extraordinary when she communicates directly a pigeon-riding ghost; most other times all she can do is listen to their Unfinished Business. In Bloodhound, she speaks to the pigeon ghosts as a matter of course. The reason for this change is never directly stated; most fans decide that she developed her ability between books to explain it.
In the introduction to the novelization of A New Hope (whose title is just Star Wars, of course), it is explicitly stated that the Emperor is a powerless weakling who is controlled by his Evil Advisors. According to Wookieepedia, the Whills got the whole story from R2-D2 about 100 years later, so that means every one of the main characters is now an established liar. The novelization, published under Lucas's name but ghostwritten by Alan Dean Foster, actually came out months before the movie.
The opening crawl of A New Hope states that "Rebel spaceships, striking from a hidden base, have won their first victory against the evil Galactic Empire." Take a wild guess if the Expanded Universe portrays more than zero Rebel victories taking place before this. So it all starts with the second line of the first-released film. And that's probably only because "It is a period of civil war." is pretty hard to screw up.
The lightsaber itself started as a ceremonial weapon, mostly used for battles between Jedis and a last resort weapon when diplomacy failed. Twenty years of expanded universe, parodies and video games later, Jedis are facing off entire armies with nothing but a lightsaber.
In the novelization to Return of the Jedi, it was stated that Darth Vader got his injuries from falling into a lava pit after a duel with Obi-Wan. This was taken for granted for decades until Revenge of the Sith revealed that Obi-Wan cut off his limbs (the remaining ones, anyway) and Vader was burned by his close proximity to the lava, but not actually falling into it Terminator-style. Lucas himself mentioned Vader's fall into a volcanic pit to Rolling Stone as early as 1977 but in the same interview Vader and Luke's dad are separate characters.
The Return of the Jedi novelization follows a draft of the movie in stating Obi-Wan and Uncle Owen were actually brothers. Nothing really contradicted it until Attack of the Clones where Owen is Anakin's stepbrother. Thus, after The Phantom Menace, a Jedi Academy novel with young Obi-Wan came out which mentioned his brother Owen.
The Force Ghost technique was implied in the original trilogy to be the standard Jedi afterlife. Even Anakin achieves it when he dies after his Heel-Face Turn. By the time new Expanded Universe material and the prequels came out, it was established that this technique was extremely difficult to perform and that Qui-Gon Jinn was the first to use it, and that Yoda and Obi-Wan learned it from him.
Taking down an AT-AT walker with the tow cable in Empire Strikes Back comes across as a crazy last-ditch gamble. In Expanded Universe, especially video games, this is used as a common tactic (probably because players would feel ripped off if they didn't get a chance to duplicate the famous maneuver). This was justified at least once by saying that as much of a crazy gamble as trying it the first time was, it worked so unexpectedly well as to become standard thereafter.
Some of the Horatio Hornblower short stories contradict the events of the published novels (most prominently the capture of the Castilla and the consequent powder burns on Hornblower's hand). C.S. Forester discouraged their reprinting because of this. He also did a couple of retcons on Hornblower's birthday (1771 to July 4, 1776) and the length of his friendship with Bush, along with shortening his acquaintance with his first wife, Maria—statements in earlier written novels imply that the marriage was due to a Childhood Friend Romancenote with all the romance being on Maria's end but Lieutenant Hornblower indicates that they first met as adults, when Hornblower was staying in the Masons' boarding house.
In the Circle of Magic series, the sources of ambient magic have become more anthropomorphized as the books go on. They always have been, to some degree (Sandry "frightens" some wool during the first book), but it's usually been a case of mages being able to relate to their own source of magic. By Melting Stones, the ocean speaks directly to Evvy the stone mage and is openly malevolent towards her. Natural events are also more tractable. In the first book, Tris nearly kills herself by trying to stop the tides along a short stretch of beach; in Melting Stones (again), Evvy is able to speak and reason with a Vesuvius-Expy volcano.
Live Action TV
Charmed, after the Wizarding School was introduced. In later seasons, they get all obsessive about protecting the Wizarding School because "where else will the children learn about magic?", even though none of the other magical characters shown in the show up to that point went there.
While it was only All There in the Manual in the first place, The Master was originally supposed to be 600 years old, and to have outgrown human features as a result of his age. However, a flashback showed him siring Darla approximately 400 years ago and looking the same, even though if he'd already stopped looking human at 200 Angel and Darla should have had the same look by the time of the series. The comics presented an alternate explanation for his appearance — while at the same time establishing him as at least 800 years old. And this explanation clashes with the similar Looks Like Orlok appearance of a vampire called the Prince of Lies over on Angel.
The different and unexplained look of werewolf Oz in Season 2 and Season 3.
In the first few episodes of Roswell, it's clear that all the aliens have all the powers, but Michael just isn't as good at using them. We even specifically see Michael heal someone's broken ankle. As the series went on, this drifted into them each having unique special powers to the point where Max being the only one able to heal people became a huge thing. This was presented as the way things had always been. This is most likely because the series started out sticking to the book series it was based on (where all of the aliens had the same broad range of powers), but soon developed into a completely different story line with the six main characters being the only thing consistent with the books.
CSI: Crime Scene Investigation has this, mainly with the character of Grissom. In the early episodes, he is shown to be a quirky eccentric with lots of connections. However, by the next season he is a reclusive intellectual with traits of Asperger's.
In the first season LOST episode "Raised By Another," a flashback shows Claire fretting that her mother will disown her if she tells her she's pregnant. The third season episode "Par Avion" reveals that Claire's mother was in a coma at the time.
The Adam and Eve skeletons introduced in season 1 are implied to be 50 or so years old and we're left with the impression that they were some loving couple who died on the island. In season 6 we discover that the skeletons are hundreds of years old and belong to the smoke monster's original form and the crazy lady who pretended to be his and Jacob's mother.
It's generally accepted by fans that the flashbacks in "Across the Sea" (where we discover the origins of the skeletons) take place around 1 AD. If this is true then the skeletons are around 2000 years old. That's a far cry from 20-50.
Aaron and Walt's importance. Season 1 and season 2 make a point foreshadowing Walt's powers. It's a non-issue in his few appearances in the later seasons. Aaron's destiny was hinted to be fairly important when the psychic warned Claire he must not be "raised by another". He gets raised by another (Kate) and there seems to be none of the dire implications the psychic hinted at.
There are some differences between how the Others act in early seasons compared to later on, which can be chalked up to the fact that the writers hadn't really decided what the Others were yet. In early appearances it seems like they were intended to have supernatural powers, most notable in Ethan's super strength and ability to pop up from out of nowhere. And while we're on the subject of Ethan, in season three Ben says that Ethan was their surgeon. Now, why would Ben send the Others' only surgeon on a dangerous mission to infiltrate the crash survivors (as he did Goodwin, who it seems he sent with the intention of getting him killed) a short time after he has found out that he has a lethal tumor on his spine? Also, in the first few seasons it was well established that the Others kidnap children, and we assume that this was the reason they took Rousseau's daughter, Alex.
There's also the fact that Ethan is apparently one of the few who grew up on the island, which makes you wonder where he got his surgeon skills. Of course, considering that the whole surgeon thing is from a throwaway line in "Stranger in a Strange Land", perhaps we should just forget about it. And you have to wonder about the Others not kidnapping Jack and co when they went after Michael.
An early Babylon 5 episode has Delenn mentioning that Minbari society is made up of two castes: warrior and religious. Later episodes show that there is also a worker caste, which becomes very important when the Minbari start a civil war. Word of God says "She just forgot to mention the worker caste. That's my story and I'm sticking to it." Just how often the other two castes forget the worker caste eventually became an important plot point. The in-canon novel "To Dream In the City of Sorrows" goes into more detail about the marginalization of the worker caste: there was an objection to them joining the Rangers, members of the other two castes would lose face if they spoke in worker dialect, and before Valen came there wasn't even a pretense of them being an equal caste.
Star Trek has several, with the fans being far more forgiving of some than others. One essay calls these "Brain Bugs" and posits that it's because of a long succession of writers either being unfamiliar with or flat-out misunderstanding what came before and as such, end up simplifying concepts and reading unintended meaning into minor details. Examples include:
Deanna Troi went from outright experiencing beings' emotions in the pilot to merely being aware of them.
Q being several different beings with the same face (never actually stated, but it was the idea the writers had and the actor's performance in the TNG pilot bears it out).
In the original pilot episode, the idea of Vulcans repressing emotion and acting on logic hadn't been thought of, and Spock seems to be a very different character because of it. While one could easily argue that the pilot episode is non-canon, the TOS episode "The Menagerie" was a Whole Episode Flashback to it. It also implied that faster-than-light travel was a new invention, when it was later established to have been invented much earlier.
In TOS, the most common time-reference was that it was set about 200 years after the 1960s. Furthermore, there had been nuclear warfare on Earth after the 1960s. So it actually made some sense that warp drive, as of the time of Pike's first visit to Talos IV, would be a fairly new thing. (It also implied that some form of FTL travel existed other than warp drive, maybe natural gates or something, because of the Valient in "Where No Man Has Gone Before" and the Romulan War. But all this kind of worked, because it gave the feel of a frontier, worlds not settled all that long, technology advancing but with the backwaters behind. TOS just simply does not fit, continuity-wise, with the other series.
The hand-held communicators got larger between Enterprise and TOS, before shrinking to com-badges in TNG.
The original series was very vague and contradictory about what century it was supposedly taking place in — offhand references implied the 22nd, 23rd and even the 28th centuries. The Wrath of Khan finally cemented the setting as being in the 23rd century, though the exactly 300 years in the future detail was established later.
Most of the well-known races in Trek are wildly different from how they were originally conceived, beginning as a complex race and devolving, from one writer to the next, into a Planet of Hats. The Ferengi, in their first appearance, were being set up as a fairly major military power; a few seasons later they were a much smaller power and quite cowardly, and by the time of Deep Space Nine, they were, for all intents and purposes, not a military power at all, and their personality had withered down to all profit all the time. Their first appearance was the first reported visual (and possibly audio) contact with a Federation citizen, whereas by DS9 (less than half a decade later in the timeline) they had been an established economic presence in the quadrant for decades and had deep-seated ties with Klingons and Cardassians. Also, while DS9's Ferengi were often amoral scumbags, their outright evil TNG forebearers dressed in Klingon-esque primitive, fur-sashed mail uniforms, acted half-feral, executed second officers as a diplomatic act, and were stated to eat sapient beings. Not long after, they started wearing wide-collared suits, dressing more like modern humans that the Feds. Also, In several early Ferengi episodes, Troi claims to sense their feelings. Later on, Ferengi are immune to telepathy/empathy.
Similarly, the Borg were, initially, all the same organic race. In the first episode they are introduced, incubators with Borg young are shown, and assimilation is used only in the sense of acquiring alien technology. In "The Best of Both Worlds", they kidnap and assimilate Picard to act as a liaison to humans — but this is done surgically and with one particular purpose in mind. By the time of First Contact (and their subsequent appearances on Voyager), they don't reproduce or even conduct scientific research of their own at all, relying on assimilation alone for both.
One Voyager episode showed some Borg children who had come out of their development chambers early and so were only partially assimilated. It's possible that children who are assimilated are kept in the incubation chambers until they reach maturity, for whatever reason.
In "Space Seed", Spock refers to the Eugenics War, which occurred in the 1990s, as World War III, whereas later episodes and spin-offs establish WWIII as taking place in the mid or late 21st Century.
Klingons started off as a stand-in for the 1960s Soviet Union and were generally very pragmatic and duplicitous in their interactions with the Federation. Beginning with Star Trek: The Motion Picture and a visual redesign of the species (which is a contentious topic all on its own), they started drifting more and more towards a "space viking" culture. By the time of Deep Space Nine and the TNG movies, they were always seen in battle armor no matter their role, were eating like wild animals (complete with the addition of prominent canine teeth), obsessed over honor and a glorious death in battle, and were basically a total reversal of the civilized but duplicitous Original Series incarnation.
It should be noted that the Klingons virtually swapped characterization with the Romulans, who were depicted as honorable and noble warrior-officers. TNG and DS9 retooled them as a duplicitous, racist empire of fairly unsympathetic villains - hell, in the Decipher CCG adaptation, their main skill was literally Treachery.
The makeup issues of various Rubber-Forehead Aliens can be seen as this. In addition to the ridges-or-no-ridges Klingon and Romulan cases, several races underwent several adjustments on the way to their current depictions. The Trill are completely different to the point that a fan theory is that the name similarity may be coincidence, and even the Bajorans originally had little Y protrusions above their noses that they lost in the first third of Deep Space Nine's first season.
One of the weirdest examples involved the rank of a single character. Miles O'Brien was formally made a character (he had been seen as an extra before) in the second season, and wears the rank pips of a lieutenant, and is even addressed as such once. Later, characters started referring to him as "Chief" because his job was "transporter chief". Then came the episode "Family" in which a character refers to him as an enlisted man, despite his lieutenant pips still very clearly shown. Finally, in the sixth season, they changed his pips to a single "darkened" pip, indicating his enlisted status, and from then on the producers and writers have declared that he was, is, and always has been an enlisted man.
In Star Trek: First Contact, Zefram Cochrane is shown as the man who not only created warp drive, but also conducted the first warp flight and made first contact with an extraterrestrial species shortly afterward. In the TOS episode "Metamorphosis", where the character originated, he was said to simply be the inventor of warp drive. No more, no less.
Also, the Prime Directive started off as something like a principle of anthropological objectivity: How do you study a culture in its natural state? By not letting them know that you're there, obviously. It also allowed Federation scientists to avoid morally-dubious "A God Am I" scenarios. But as the series progressed, it became treated more and more as a moral philosophy, until, on Enterprise, it finally assumed a near-mystical quality with Starfleet not wanting to interfere with the "destinies" of primitive cultures.
In "Where No Man Has Gone Before", the second Trek pilot, Spock says that one of his ancestors married a human female, implying some distant relative. Somewhere along the line they decided that Spock's mother was human, and the Maligned Mixed Marriage of Spock's parents is now an essential part of his character. Why Spock avoided mentioning that his mother was human is left to the imagination, though it is possible that at that point he was just trying to cover up a part of his heritage he was ashamed of.
Comparing the instances where distance, time and warp factor are all mentioned, you get wildly varying values for how fast warp speed actually is. One velocity mentioned in the original Star Trek would have gotten the Voyager home within months. To mention another instance, in Enterprise warp 3 is more than ten times faster than warp 3 in The Next Generation. There is an official mathematical formula for calculating the warp speeds, but it seems like the show's own writers do not bother to use it. (One get-out clause the writers have proposed is that warp speed definitions changed between TOS and TNG. ENT, being a prequel, presumably uses the original scale.)
When Bajorans were first introduced with Ensign Ro Laren on TNG, she wore her earring on her left ear. When the Bajorans were further fleshed out in DS9, they all wore the earring on the right, apparently due to the Bajoran belief that the "pagh" (essentially the soul) resides in the left ear. The novels state this was due to Ro Laren not following the main Bajoran religion.
When the Daleks first appeared in Doctor Who they threatened a small tribe of people and, themselves, constituted just an isolated group in one city. In their next appearance (supposedly set earlier in history), they had successfully conquered Earth. In their third appearance they had Time Travel. In their fourth appearance, they had Time Travel and threatened Earth's entire galaxy (and probably other galaxies besides.) Along the way, the Daleks became increasingly machinelike in their speech. Destiny of the Daleks described them as literally, organic creatures which had literally become machines. (Later continuity would ignore this development.)
More significantly, the origin of the Daleks changed; they were originally the mutated survivors of a war, and were later shown to have been deliberately created by Davros. And both stories were written by Terry Nation, who created the Daleks. This is somewhat justified as Davros' creation of the Daleks was explained to originally been designing a travel machine for the eventual mutated form of the Kaleds as a result of the war. He then just decided to mess around with the mutants to make them think as the Daleks now do.
The Time Lords, the Doctor's people, established as beings who never ever ever interfered with other planets, had the Doctor doing errands for them within two years of real time. This later got Retconned away as Time Lord covert ops missions. As well, after the Time Lords were introduced (previously the Doctor only belonged to a nameless and mysterious Human Alien species) he often ran into people and civilizations who knew of them.
When the mythic Time Lord Rassilon is first mentioned in The Deadly Assassin, the Doctor has apparently never heard of him. As the backstory of Rassilon evolved over the years, this became less and less believable, until it currently appears that Rassilon is not only as famous as, say, Jesus, but that the Doctor knew him personally.
It is now generally accepted that Timelords automatically regenerate when mortally injured, but it wasn't until the FIFTH regeneration that this happened. Hartnell was renewed by 'part of the Tardis'. Troughton suffered a 'change of appearance' (often supposed now to be a forced regeneration). Pertwee only regenerated after being given a nudge by K’anpo (although it's finally termed 'regeneration'). Tom Baker merged with a mystical future version of himself. Only with Davison's regeneration onwards has the process been regular and automatic (and even Davison's Doctor questioned whether his death would trigger regeneration - "I might regenerate - I don't know".)
However, evidently Time Lords can still stop themselves from regenerating on purpose, as the Master did in Last of the Time Lords.
Battlestar Galactica (Classic): The war with the Cylons has been going on for millennia, except when it's been going on for only many years. One episode specifically says Starbuck was orphaned about 20 years ago, in one of the first Cylon raids.
The miniseries says that after the first Cylon war, the Cylons left and made their home on a distant planet. This is brought up again in Season 2 when it is explained that the Resurrection Ships allow Cylons to download into new bodies when far from the Cylon homeworld. After that, the idea seems to have been quietly dropped. Season 4 introduces a spaceborne "Resurrection Hub," which is said to be essential to all Cylon resurrection everywhere, and the homeworld is never mentioned. In the last few episodes, this is brought up again, although it is changed a bit more: the Cylons had been living on the 'Colony', which was more like a large space station than a planet.
This trope can sort of be applied to the show's visual effects, too. At the beginning of the series — the miniseries through to Season 2 — there was a lot of emphasis on the spacecraft behaving like spacecraft actually would, with noticeably unique — and awesome because of it — space battles in amongst the politics and drama. From Season 3 onwards, the battles got gradually more and more glitzy and dominated by the Rule of Cool. The battle of the Colony, the final battle of the series, had much more in common with the destruction of the second Death Star than the more understated and nuanced battles in the first two series.
Six's glowing spine that lights up during sex in the mini.
The population of the 12 Colonies was stated as 20 Billion in the Resistance webisodes. Season 4 mentioned that the population was 50 Billion. It's an easy one to miss, as not many people have seen The Resistance.
When the Genii first appeared on Stargate Atlantis, they appeared to be a Space Amish society until it was discovered they were actually far more advanced and kept it a secret by living in Elaborate Underground Bases. Teyla, who had been friends with the Genii for years, complained that they never told her and they replied "that is our way". Several episodes later, the Genii were making no effort to hide their advancements and by the fifth season it seemed to be common knowledge that they were a major power.
This is plausibly explained as them simply abandoning their secrecy since it had already gotten out. With the Atlantis expedition knowing the truth about them and considering them enemies (and therefore quite likely to blow their cover anyway), what would be the point of keeping up the ruse?
In Frasier, Hester comes off very differently in her appearance in Cheers than in her flashbacks and stories in Frasier. She threatens to kill Diane, for one thing, while on Frasier she was always touted as a bastion of class and common sense (although this could be a case of Never Speak Ill of the Dead). Also, she seems to be a rather soft-spoken, frail, grandmotherly woman who Frasier treats with great gentleness and care on Cheers, whereas she was described as a bold, intimidating matriarch on Frasier. Frasier's claims on Cheers that he's an only child and his father is a dead psychiatrist were eventually explained as him being in a bad mood with his family and just lying.
Boy Meets World: As Cory and Topanga's Romance Arc progresses, their history seems to drift also. In the early years of the show, Topanga was a Cloud Cuckoo Lander whose crush on a very unamused Cory was Played for Laughs. Later, there are many references to them having been totally in love since they were in Pull-Ups. She is shown in an early episode giving him his first kiss though. This is handwaved later by saying that Cory and Topanga were best friends when they were really little until Cory was teased by other little boys for the friendship. As a result, he abandoned the friendship and didn't rediscover his feelings for Topanga until puberty. At one point, his big brother even takes credit (laughing about it) for convincing little Cory that girls were gross, contributing to the temporary split with Topanga.
Red Dwarf starts off saying that Lister never dated Kochanski, but later says that he did but that it wasn't very successful. The reason for this is that the episode where he says he did date her is based on part of the spin-off book "Infinity Welcomes Careful Drivers" which takes place in a somewhat alternate continuity. In a similar way, Kochanski is introduced in Series 7 by being from a parallel universe, which handwaves the fact that she's played by a different actress. However, flashbacks from this point on to before Series 1 have the same actress play Kochanski, which was understandable as they couldn't get the original actress, but it still doesn't make sense in continuity.
In the episode "The One With The Prom Video", Chandler appears to be seeing Fat Monica and college age Ross's perm for the first time, just like Joey, and mocks College!Ross's music. Later flashbacks would establish that Chandler was Ross's roommate at the time, spent Thanskgiving with the Gellers, was in Ross's band and after some hairy incidents also became friends with Monica. He only lives across the hall because Monica tipped him off that the apartment was free.
The age of the friends also changes. Season 1 has Monica and Rachel say they're 26, making Ross, Chandler and Joey 27. (Phoebe is murkier). However by Season 7 Monica and Rachel are 30, and the guys are 31, making them 24 and 25 in Season 1, which is supported by flashbacks of the dates they attended high school/college. It looks like in early seasons the writers planned for the characters to be older, realized it didn't work and lopped a few years off everyone's ages.
Much of LEGOBIONICLE's early media got contradicted, at times very early on, due to its inconsistent nature. This is because originally, LEGO didn't know that the line would be one of their long runners, and the line was one of their first full-blown multimedia IPs, so its continuity had a rough start.
Some inconsistencies were actually planned for — for example the original backstory being revealed as a legend forged by the village priests.
Early card games described characters and history completely differently than what was seen in the comics and online content. Most of the discrepancies have simply been declared non-canon, or examples of Advertising Only Continuity.
When LEGO was forced to change the name of the villagers from Tohunga to Matoran for legal reasons, they gave it a story justification, but after a while stated that Matoran has always been their name.
The canisters that the Toa arrived to the island in were originally stated to have fallen into the sea when Takua gathered the Toa Stones, and supposedly Kapura was there to witness it. Later, it was explained that the canisters had been floating in the ocean for a 1000 years, and the Stones have only beaconed them to the island. Kapura, at the time when the cans were originally launched, had been lying comatose in a storage sphere, along with the rest of the islanders.
The three virtues, Unity, Duty and Destiny, were introduced in the third year, even though later material explained that they have been the most fundamental parts of the universe all along. They've been retroactively written into the "Legend of Mata Nui" backstory after that.
Also, in the first game, when Phoenix and Grossberg first meet, it's implied they never met, even though he appears in that first case of the third game.
In the Baldur's Gate series, a great many things don't quite fit together. First comes Imoen, of whom we cannot be quite sure when we met her or why she can be revived after dying even though her heritage should make death irreversible. In the Throne of Bhaal we meet a fully grown dragon of about the your age (20 years) and even with mature offspring by his side. At least what your stepfather's letter told you about your mother may be explained away as an attempt to not further upset you.
Except there's nothing saying that all the Bhaalspawn are the same age. After all, Bhaal's death had been foretold centuries earlier, presumably he could've started making heirs early enough for a dragon to grow up.
Curiously, if Naked Snake dies at any point during Metal Gear Solid 3: Snake Eater, the words "SNAKE IS DEAD" slowly change to "TIME PARADOX".
The Crysis series has gone through this in regards to the main alien enemies, the Ceph. In the first game, they were jellyfish-like blue critters that thrived happily in very, very low temperatures and environments with little gravity. In fact, they considered Earth inhospitable enough that you never fought them in person outside a controlled environment. Also, most of their weapons were cold-based. Come the second game and they're orange, walking around outside with the help of powered armor, no longer seem to mind the temperature, and use fusion-type weaponry and biological warfare as opposed to their original cryo-weaponry. As the aliens in the second game are very effective villains, opinion is divided as to whether or not these changes were for the better.
Touhou: Most of the games made before Phantasmagoria of Flower View don't fit well with later canon. The first five have just been ignored. The sixth through eighth are definitely canon, but present Gensoukyou as a large place, filled with mystery and danger, while later worldbuilding would establish it as small and human deaths as rare.
In Mass Effect 1, Cerberus was presented as a dastardly lot carrying out unethical experimentation for little good reason. When Mass Effect 2 came about and players were forced to work with them, the members with which you now encountered being more moral sorts, attempts were made to paper over the difference by claiming those that appeared in the first game were rogue elements. Not everyone bought the explanation. Mass Effect 3 revealed that the Illusive Man collected the most sympathetic members he could find to manipulate Shepard.
Narrowly averted in Domain Tnemrot. In a blog post, Herbert says the original 4th chapter gave a history that conflicted with the one mentioned in the About page, so he changed everything around at the last second.
Homestuck: In one early conversation between Karkat and Sollux, the two trolls insult each other by saying that the other is repulsive to the opposite sex, and on another occasion, Feferi immediately assumes that Eridan's crush is female, before considering that it might be male. Both of these conversations seem to imply that troll society is heteronormative; however, it is later established that the trolls are all bisexual, and don't even have a word for monosexuality. It's not too hard to come up with an in-universe justification - it would be consistent with canon if some characters had mild preferences for one gender, and all of those characters had opposite-sex love interests - but it's clear that Hussie hadn't come up with the idea of all trolls being bi until later on.
Similarly, it's later established that gender is basically purely aesthetic to trolls with no different reproductive capabilities and no real social or cultural attachments. However, early pages in Hivebent seem to disagree with this, such as in one moment where Tavros was hurt and Karkat yelled at him to 'STOP PLAYING GAMES FOR GIRLS'. Theories have been imagined, including one rather popular one that women actually tend to be more aggressive and that Karkat wasn't insulting his choice of game so much as his ability to play something so dangerous, but it's still almost certainly drift going on here.
And there's the matter of the trolls' blood-based Fantastic Caste System. Later it turned out to be an integral part of their society with castes strictly enforced. Very early on, though, the hierarchy was portrayed much more casually, with Sollux even being unaware of the order the colours go in.
The Order of the Stick: This very early OoTS comic implies that Roy's father and mother share realms in the afterlife, which they are later shown not to. Luckily, it's early enough that you can ignore it, and it's only one line (which has possible Fridge Brilliance attached).
In earlyOzy and Millie comics, Millie lived with both her parents. Much, much later, we discover that her father is a pirate who ages backwards.
Throughout Red vs. Blue, the role and scope of Project Freelancer, how common AIs are, and what happened before the first episode have drifted quite a bit. There have been few explicit retcons, if any, but implications from earlier seasons—such as every Freelancer having an AI—have been proven incorrect—there were less than ten AIs implanted in agents. More notable are several statements from the miniseries Out of Mind inconsistent with later series, which has largely been dismissed as messed-up or misinterpreted memories of Tex.
Sarge finally learns Spanish in the Relocated miniseries. He has apparently forgotten it by Season 11.
The pilot episode of Futurama stated that all jobs were selected for everyone by the government, everyone had "job chips" implanted in their hands, and leaving your job was punishable by death. Nowadays, the job chips seems to function mostly as a form of ID, with everyone taking the job they want.
In addition at the end of the pilot they were escaping the police and Nixon in an explosion of fireworks. This issue is never brought back up in the following episodes.
A later episode lampshades the job chips when they are fired from Planet Express and take up their old jobs again by having Leela explain the concept of career chips to a dumbfounded Fry.
Another early episode had Bender joining a robot religion led by Preacher Bot and swearing off alcohol for the religiously acceptable synthetic oil. And yet the very first episode established that alcohol is necessary for a robot to function (there's even a legal limit that robots have to be above), and Preacher Bot is even seen handing out alcohol to homeless robots in the first Christmas Episode. This is never addressed.
They argue in the episode that robots are also able to use 'mineral oil' instead of alcohol. Presumably alcohol is either cheaper or easier to produce (or both).