In the Asterix comics, Obelix's birthday is celebrated in Obelix and Co., just Obelix's. But in Asterix and the Actress, it is revealed that Asterix and Obelix were born on the same day and they celebrate their birthdays together.
In one issue of Bone, Rocque Ja cuts off Kingdok's tongue, and it's explicitly stated he can't speak with his tongue missing. Then, in a later issue, Kingdok is able to speak without any explanation given. It's later heavily implied that the Hooded One was giving Kingdok the ability to speak without a tongue, as her brief return to death made his speech near incomprehensible.
Ghoul Goblin: In Changes, which happens after Ghoul Goblin, Harry states that he's never seen a goblin before. However, in Ghoul Goblin Harry interacts with a goblin.
Harry makes contact with Lea in an attempt to stop Puck— only problem is that this takes place before Changes, and up until then, Lea was still imprisoned in the ice garden atop Arctis Tor in an attempt to purge her of Nemesis.
Molly examines the bodies of the two young women attacked by Puck and says their souls were removed from their bodies, indicating White Court vampire involvement... despite White Court vampires feeding on emotions and not souls.
Dog Men: There is a scene in which Listens-to-Wind shapeshifts in front of Harry and he's astonished by how easily he does it. The problem is Dog Men is set before the events of Turn Coat, which famously depicted Listens-to-Wind saving Harry from a skin-walker and that marking the first time Harry ever saw Listens-To-Wind shapeshift.
Fables. This is done as a plot point. It used to be 'John of All Fables' but the 'author' made a typo so the universe created the Loveable Rogue Jack of All Fables. Jack meets John later on. Chaos ensues, which it usually does around Jack.
In issue #2 of Pocket God, the pygmies bury Klik when they think he's permanently dead; marking his burial site with a gravestone. However, in issue 14, everyone but Klik is perplexed when they come across some graves; not knowing about burials because they are immortal and never had to bury one of their own.
Rivers of London: In volume 4, Detective Stories, minor character PC Purdy from the novelMoon Over Soho is given the first name "John". Unfortunately, in the book his first name was Philip.
Serenity: Leaves on the Wind: One scene has a New Resistance member suggesting Malcolm Reynolds is hiding out on his homeworld, Shadow, with Bea retorting that Mal is too smart to hide at his house. Other material, including the RPG, stated that Shadow was glassed by the Alliance during the Unification War.
Chekhov and Sulu's origin story includes Red Squad, despite their appearance in DS9's "Homefront" and "Paradise Lost" implying they had only recently been formed.
The Countdown to Darkness miniseries chronicles the Enterprise crew's immediate mission (dealing with the discovery of former Captain Robert April) before they head to Nibiru (which is where the events of Into Darkness begin). However, the video game adaptation (which is also considered canon by Paramount) has the crew dealing with a immediate threat from the Gorn before they go to Nibiru.
In The Smurfs, the story The Finance Smurf introduces the money system and the Smurfs are revealed as not knowing what money is at all. This contradicts earlier stories, such as The Egg and the Smurfs where a Smurf makes a wish to become "rich" — and ends with jewels and money as a result — and in Smurf Stories where a Smurf creates a machine that can turn hazelnuts into gold coins and the Smurf tells Papa Smurf he'll use the coins to buy more hazelnuts.
The first issue of Comico's 1980's Comic-Book Adaptation of Star Blazers, set after the events of the second season of the TV series, shows Sparks at his post in Engineering. Sparks died at the end of the first season, and his death was an important plot point.
In a Teenage Mutant Ninja Turtles comic — early in the "City at War" arc — the Foot Soldiers are shown knowing the location of the Turtles' lair since they had apparently "raided it before". This event happened in the first theatrical movie — never in the Mirage comics.
In the 2005 IDW Transformers continuity, Grimlock doesn't have his famous Verbal Tic until after the War, as shown in The Transformers: More than Meets the Eye. He has it in Autocracy, though, meaning that he picked it up, lost it for a few million years, and then gained it again.
Starscream gets outed as a Decepticon spy in the Senate in other pre-War comics, then accepted back for Autocracy for some reason.
Transmetropolitan's resolution famously revolves around a picture taken by a minor character. Unfortunately, said minor character is given the camera long after the event she is supposed to have taken a picture of.
Matt Olsen of the W.I.T.C.H. comic series is one of the worst examples of this. When he first appears, he's a student with a thing for guitars, has a grandfather who owns a pet store and is utterly shocked when his girlfriend, Will Vandom, reveals her secret identity as a Guardian. However, come the second chapter of the New Power storyline and it's revealed that he's actually from Kandrakar, knows magic and already KNEW Will and her friends were Guardians. And there's been nothing to try to fix the previously established backgrounds.
