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Archie's Sonic the Hedgehog comics introduced an original character named Geoffrey St. John, who at one point in the comic was in a romantic relationship with Sally Acorn, a character from the 1993 "Sonic the Hedgehog" animated series. This has been met with controversy from fans, because Sally was, at the earliest, 15 years old at the time of the relationship. While Geoffrey's age was never stated in the comic leading some to argue that a seemingly nonexistent age gap would be irrelevant, his creator Ken Penders claimed in 2015 that the character was 21 years old at the time of Sonic the Hedgehog Issue #46, which released in May 1997. In the Sonic-Grams fan letter section of that same issue, one fan letter asked if Sally is 14 or 15 years old, with the editor Justin Freddy Gabrie confirming she is 15 (it should be noted that while Gabrie incorrectly lists the wrong age for Bunnie Rabbot in this response implying others could be wrong, Sally's age is consistent with her being the same age as Sonic throughout the comic). All of this information is made significantly worse when Geoffrey is shown making out with Sally during the same issue, which they also did in other issues around this time. To complicate this further, in Issue #20 of the spin-off comic Knuckles the Echidna, which released in January 1999, it's shown that Geoffrey is older than Sally's older brother Elias Acorn, who was 21 at the time of the relationship, through two scenes. The first is when Geoffrey calls him a "kid" in the present, and the second is through a flashback showing Geoffrey as a physically older child than Elias, who was 5 years old in this flashback. Both aforementioned issues were written by Penders, meaning that even if his original claim of Geoffrey being 21 was incorrect, it implies that he retconned Geoffrey to be older than that at the time, making the age gap larger.
This controversy worsened even further when Penders revealed in 2019 that he had planned at some point for a story involving Geoffrey taking Sally's virginity. While he acknowledged that this was a story that couldn't be told in the comic, as content found in the series had to remain within the realm of a G-rating, he attempted to justify the relationship in the context of a historical drama setting by saying:
"There are states here in the US where a 13-yr-old can marry someone in their 40’s, as repugnant as that reality is. Sally was 16 to Geoffrey’s 20, so I don’t see a problem given the relationship in Royal history."
However, considering the cited source material, this justification is fundamentally wrong as the actual implied age gap would be larger than the 4 years Pender suggested (Sally's 15 to Geoffrey's at least 21), leading fans to accuse Geoffrey, and Penders by extension, of being a pedophile.
In Kinoko Nasu's first draft of Fate/stay night that he wrote while in high school, he had planned for Saber to be a man and the player character to be a woman in glasses. While the two genders were eventually flipped for the final game, this idea was revisited in "Fate/Prototype", an original video animation released as part of the Carnival Phantasm OVA collection. Fate/Prototype portrays Saber and the primary Master as described in the early drafts, but as of now, the full story of "Fate/Prototype" has yet to be told, with the animation and short story details being the only known aspects of this particular adaptation.
One particularly infamous lyric in PaRappa the Rapper is in Prince Fleaswallow's rap, where he claims to have "been working here since [his] mama was a baby". While it is simply an exaggerated simile and not an actual piece of world lore, it has still been the source of mild chuckles from players for its unintentionally disturbing undertones if taken literally.
When music from PaRappa the Rapper was played by an orchestra at Sony's 23rd Game Symphony Japan concert in 2018, the lyric would be revised from "Since my mama was a baby" to "Since your mama was a baby", a more fitting lyric as PaRappa is supposed to be a young adult and Fleaswallow is presumably significantly older.
In the original Star Fox on SNES, Venom was said to be a beautiful, green planet in the vein of Corneria before Andross, after being banished by Corneria due to his dangerous experiments, invaded and ruined it, transforming it into a dark, polluted world of military machines, all while enslaving its inhabitants who he drafted into his new army. Star Fox 2's Venom stage on Expert mode would actually depict Venom in its lush green state again, indicating that it was being terraformed back into its original state.
Star Fox 64, being a reboot of the first game, would essentially retcon all of this, and claim that Venom was already a desolate wasteland to begin with, which is the entire reason General Pepper banished Andross there after the latter nearly destroyed Corneria with his weapons. That being said, Star Fox Command would later reveal that during his banishment on Venom, Andross had actually created a terraforming device that he planned on using upon Venom as a means to transform it into a beautiful green world similar to Corneria, for prosperity and to also give his heirs and descendants a home to live happily in. This is essentially an inverse of his original SNES backstory, where he's now trying to save Venom and turn it into a hospitable world, as opposed to invading and transforming it into a polluted wasteland.
Upon the release of Sonic Chronicles: The Dark Brotherhood, Ken Penders, a former writer on the Archie Comics Sonic comics, sued Sega and EA for supposedly using Sonic character concepts he had independently trademarked prior - particularly the Nocturnas Clan, a futuristic echidna tribe which he deemed as too similar to his own Dark Legion, a futuristic echidna technocracy. This lawsuit came months after Archie Comics filed their own suit against Penders due to a breach of contract after the trademarking, causing Archie to allow their contract with Sega to expire so they could negotiate new terms for the rights to create Sonic comics. This legal fiasco ended in Archie settling the case with Penders, losing the exclusivity to produce Sonic comics after negotiations with Sega, and causing them to write the "Super Genesis Wave", a super-charged energy blast utilizing the Chaos Emeralds that acted as a massive continuity rewrite where over 500 original characters and concepts created by Penders and other writers for the Archie Sonic comics were retconned. The Sega case on the other hand ended in a stalemate due to the statute of limitations, and will not be able to continue unless Sega uses characters from The Dark Brotherhood again.
During his victory animation, Double D will toss his sock hat in the air, revealing his hair, seemingly answering a popular mystery from the Ed, Edd, n' Eddy cartoon. However, this should not be considered canon to the show, as Double D's head was intentionally never officially revealed on the show. The game was possibly made by a separate group in Cartoon Network’s American division, while the show was produced by a.k.a. Cartoon in Canada.
According to Takaya Imamura in a 2011 Nintendo Dream magazine interview, Fox McCloud's mother is actually still alive and well on their home planet of Papetoon. This is in contrast with the 1994 Nintendo Power comic series, where it was revealed that Fox's mother (named "Vixy Reinard") was accidentally killed by a car bomb planted by Andross that was intended for her husband ("James" as he would referred to in the games starting with Star Fox 64).
According to Imamura, Fox's mother disapproved of her son following in her husband's footsteps and potentially getting himself killed the same way, and thus they have become estranged from each other, though they haven't exactly broken off from each other completely. Imamura even hints that she's secretly supporting her son's actions from behind the scenes.
Garfield's Scary Scavenger Hunt features a cameo from Lyman, Odie's original owner who disappeared from the Garfield comics in 1983, where he is chained up in the basement of the haunted house. This somewhat lines up with a joke in the 1998 book 20 Years & Still Kicking! Garfield’s Twentieth Anniversary Collection, where a comedic list of reasons for Lyman's disappearance was provided, with "Don't look in Jon's basement!" listed as #1. The difference from the book being that the Scary Scavenger Hunt game does not take place in Jon's house, nor is the haunted house ever said to belong to the Arbuckle family.
Lyman also makes a second cameo in the game's sequel Garfield's Scary Scavenger Hunt II: Donuts of Doom, where his severed head can be found inside of an oven.
Lyman would eventually reappear in The Garfield Show where he was said to have left for Australia to find cryptids and protect animals from poachers.
Article on Lyman's appearances in the Garfield franchise (Please note that the source gets the release date of the Scary Scavenger Hunt games incorrect): https://melmagazine.com/en-us/story/lyman-garfield
When Prince Florian was first revealed in the June 2023 Nintendo Direct for the game, some fans believed that he was either a callback or reimagining of Prince Haru, a character that only appeared in the 1986 anime film "Super Mario Bros: The Great Mission to Rescue Princess Peach" who transforms from a dog known as Kibidango into a human. This prospect was seen as troubling by Mario fans who partake in shipping, with some believing that Mario and Peach would be retconned as no longer being romantically interested, with Florian taking Mario's place as Peach's boyfriend, as Haru was in the movie.
Upon the game's release, Florian would not show any romantic interest in Peach, nor transform into a human, with their only similarities being that they are princes of flower kingdoms and Florian's facial structure baring a loose resemblance to that of Kibidango.
According to series producer Tetsuya Nomura, one reason that Mickey Mouse's role was limited in the original Kingdom Hearts was because around the same time as its release, Capcom owned the license to use Mickey Mouse for the game Disney's Magical Mirror Starring Mickey Mouse. The developers persisted and were eventually given the go-ahead to add him into the game "as long as [they only had him in] one scene, from far away, as a silhouette, with him waving his hand or something". As such, Mickey only appears briefly and seen from behind near the end of the game, helping Sora and Riku seal Kingdom Hearts itself.
Mickey's perspective of this event also appears in Kingdom Hearts 0.2 Birth by Sleep: A fragmentary passage. The reason that Mickey loses his shirt is to partially keep the continuity of the original Kingdom Hearts that showed Mickey in his classic shirtless look.
Matilda from Angry Birds was originally designed as an unnamed male bird, but was changed to female when higher ups at Rovio realized that male birds do not lay eggs. The Valentine's Day season of Angry Birds Seasons gave Matilda a girlfriend, which, after the change, retroactively gave the unintended implication of Matilda being a lesbian, despite actually being straight and later marrying Terence in the film series. When Matilda was redesigned for the 2013 animated webseries Angry Birds Toons, she would gain the pink cheeks of her former girlfriend. Angry Birds Seasons was removed from app stores in 2019, completing the retcon of the girlfriend character. Despite this, the Angry Birds franchise would introduce LGBTQ+ side characters and support LGBTQ+ fan works in later years.
In 2011, Bandai Namco created the "United Galaxy Space Force" series that retconned and merged many of their futuristic space games that were previously unrelated to each other into a single continuity. As of 2014, the timeline connects together the plots of numerous games and series including (in chronological order on the timeline) Ace Combat 3: Electrosphere, Cyber Sled & Cyber Commando, Burning Force, Galaxian, Bosconian, Bounty Hounds, Starblade, Dig Dug, Baraduke, Mr. Driller, Star Luster & Star Ixiom, Mizuiro Blood, the cancelled game "Starblade - Operation Blue Planet", Shin-Gun Destroy! Girl's Tank Battalion, the cancelled game "New Space Order", and Thunder Ceptor & 3-D Thunder Ceptor II.
In the original Star Fox on SNES, Venom was said to be a beautiful, green planet in the vein of Corneria before Andross, after being banished by Corneria due to his dangerous experiments, invaded and ruined it, transforming it into a dark, polluted world of military machines, all while enslaving its inhabitants who he drafted into his new army. Star Fox 2's Venom stage on Expert mode would actually depict Venom in its lush green state again, indicating that it was being terraformed back into its original state. 
During his victory animation, Double D will toss his sock hat in the air, revealing his hair, seemingly answering a popular mystery from the Ed, Edd, n' Eddy cartoon. However, this should not be considered canon to the show, as Double D's head was intentionally never officially revealed on the show. The game was possibly made by a separate group in Cartoon Network’s American division, while the show was produced by a.k.a. Cartoon in Canada.
According to Takaya Imamura in a 2011 Nintendo Dream magazine interview, Fox McCloud's mother is actually still alive and well on their home planet of Papetoon. This is in contrast with the 1994 Nintendo Power comic series, where it was revealed that Fox's mother (named "Vixy Reinard") was accidentally killed by a car bomb planted by Andross that was intended for her husband ("James" as he would referred to in the games starting with Star Fox 64).
Garfield's Scary Scavenger Hunt features a cameo from Lyman, Odie's original owner who disappeared from the Garfield comics in 1983, where he is chained up in the basement of the haunted house. This somewhat lines up with a joke in the 1998 book 20 Years & Still Kicking! Garfield’s Twentieth Anniversary Collection, where a comedic list of reasons for Lyman's disappearance was provided, with "Don't look in Jon's basement!" listed as #1. The difference from the book being that the Scary Scavenger Hunt game does not take place in Jon's house, nor is the haunted house ever said to belong to the Arbuckle family.
When Prince Florian was first revealed in the June 2023 Nintendo Direct for the game, some fans believed that he was either a callback or reimagining of Prince Haru, a character that only appeared in the 1986 anime film "Super Mario Bros: The Great Mission to Rescue Princess Peach" who transforms from a dog known as Kibidango into a human. This prospect was seen as troubling by Mario fans who partake in shipping, with some believing that Mario and Peach would be retconned as no longer being romantically interested, with Florian taking Mario's place as Peach's boyfriend, as Haru was in the movie.
Matilda from Angry Birds was originally designed as an unnamed male bird, but was changed to female when higher ups at Rovio realized that male birds do not lay eggs. The Valentine's Day season of Angry Birds Seasons gave Matilda a girlfriend, which, after the change, retroactively gave the unintended implication of Matilda being a lesbian, despite actually being straight and later marrying Terence in the film series. When Matilda was redesigned for the 2013 animated webseries Angry Birds Toons, she would gain the pink cheeks of her former girlfriend. Angry Birds Seasons was removed from app stores in 2019, completing the retcon of the girlfriend character. Despite this, the Angry Birds franchise would introduce LGBTQ+ side characters and support LGBTQ+ fan works in later years.