In 2024, Ubisoft faced controversy over two instances related to the game's marketing prior to its release being delayed. The first instance revolved around them using a flag created by the Sekigahara Teppo-tai, a Japanese historical re-enactment group, as part of the game's concept art and marketing materials without the group's permission. Ubisoft Japan would later issue an apology for this, agreeing to remove the flag from the game's website, but stated that it would likely remain in the concept art as part of the game's printed art book, something that the Sekigahara Teppo-tai would later request be removed as well. On July 23, Ubisoft posted an apology to Twitter for including material in their marketing that "caused concern within the Japanese community".

Two months after this statement, Ubisoft would face criticism again for a collectible figurine produced by PureArts featuring the game's protagonists Yasuke and Naoe standing in the ruins of a one-legged torii gate. This drew ire from critics who were already upset over Ubisoft's handling of the game's historical background, as the only known one-legged torii in Japan is located at the Sannō Shrine in Nagasaki. This torii was one of the few surviving structures after the United States' atomic bombing of the city in 1945, and became one-legged as a result of it being within 800-900 meters of the explosion's hypocenter. On September 24, just a few days after the figurine's announcement, Ubisoft would cancel their appearance at Tokyo Game Show for "various circumstances" (likely including these prior marketing controversies among other development factors) and later announce that the game's release would be delayed into February 2025. PureArts' pre-order page for the figurine was removed from their website around the same time and is still unavailable as of October 8.

The V.I.P. Bot "Robotic Sucker" (based on the titular character from Mister Mosquito) is depicted irritating Astro Bot as he is trying to take a bath. This appears to be a reference to Stage 4 of Mister Mosquito, which infamously involves the player attempting to suck blood from Rena Yamada as she is trying to take a bath.

While it's not known to have been explained by the developers, Maria's outfit in the original game bears a near-identical resemblance to one worn by American pop singer Christina Aguilera at the 1999 Teen Choice Awards, which were held in August 1999, two months after the game began development. Further suggesting this connection, Maria is also Aguilera's middle name. Maria's outfit would be redesigned for the game's 2024 remake, but the original outfit still appears during a brief scene where she finds it while raiding a closet and asks James if she would look good in it, to which he hesitantly responds: "Umm... Sure."

Originally, Donatello's Super Move was intended to be slightly different. Instead of driving the Turtle Van and shooting lasers at opponents with the other 3 Turtles, he would've perched atop the van alone, remote in hand, and rammed opponents directly.

During development, Wolves were meant to have much more complicated behavior. Every new match would have wolves start the game by forming a pack and then wandering across the map, seeking food sources while avoiding towns. Their level of aggression would vary based on their level of hunger. Furthermore, players would be able to hear howling in the background at points, the frequency of which would hint at the threat the wolves posed.

The arcade version contains an unused death animation for Sayo, depicting her falling to the ground before bleeding profusely. The animation was likely cut due to its uncharacteristic violence compared to the rest of the game.

One prisoner that players may encounter is Sean Cums, a parody of American rapper and business mogul Sean Combs (also known by the stage names Puff Daddy, P. Diddy, and variations thereof). In addition to resembling Combs in appearance and name, the character's role as a prisoner is a reference to Combs' highly publicized legal issues and sexual assault allegations starting in late 2023. These events culminated one week after the game's release in September 2024 with his arrest and indictment on charges of sex trafficking, racketeering conspiracy, and transportation to engage in prostitution.

Twin Breaker: A Sacred Symbols Adventure features characters based on Colin Moriarty and Chris "Ray Gun" Maldonado, the hosts of Sacred Symbols, a weekly podcast dedicated to discussing modern PlayStation consoles and games. Moriarty was credited as the game's writer, and would join developer Lillymo Games as its Chief Creative Officer three months after the game's release when he acquired a 49% minority stake in the company.

When Astro Bot released, many players noted how there was no reference to Cloud Strife from Final Fantasy VII despite how important that game was to the original PlayStation, or any sort of Square Enix content in the game for that matter. During an interview with Game File, Nicolas Doucet (studio head of Team Asobi) hinted that the team had considered adding a cameo from Cloud, but were unable to get permission from Square Enix, stating it was "difficult to comment on that".

When performing Homelander's "What Happens If?" Brutality on any other character, he will say a generic Brutality quote. But if performed on Kenshi, Homelander will say, "Another useless fucking blind guy." This is a reference to a quote from the TV series "The Boys" in a scene where Homelander abruptly kills Blindspot, a blind superhero. The name and animation of the Brutality also references how he killed Blindspot.

The Special Coins that appear throughout the game were directly inspired by the DK Coins in the Donkey Kong series. Lead developer Dopply revealed this while watching a livestream of Arzette: The Jewel of Faramore by Frich's voice actor, Vinny Vinesauce, posting a comment in his Twitch chat after he highlighted the similarities.

According to a 1995 Gamest Magazine interview with programmer Katsunori Itai, Virtua Cop's targeting reticle and zooming camera were inspired by a commercial for Kilimanjaro coffee that producer Yu Suzuki saw.

Among the files uncovered in the 2020 Gigaleak, a massive breach of internal server data from Nintendo, are early assets for characters who do not appear in the final game:

• Early textures for Wisp and Blathers. Given that both characters would later debut in Animal Crossing and Doubutsu no Mori e+, the presence of these assets reveals that they were originally planned for the N64 game before being held off and redesigned for the GameCube ports. Both early models feature different faces for the characters, with Blathers in particular resembling Celeste, who would debut in Animal Crossing: Wild World (implying that her design likely drew inspiration from Blathers' scrapped N64 model).
• Textures for a scrapped female cat villager with the internal ID CAT13. As villagers were not originally intended to change clothes, her default outfit, a Beatnik shirt, is included in her texture pack. However, no other data for her is present, leaving it unclear what her personality was going to be. The CAT13 ID (also written as CATD in hexadecimal) was ultimately given to Ankha in Animal Crossing; it is unknown if the original CAT13 evolved into Ankha during development or if she was simply assigned the ID for the sake of convenience. In Wild World onward, which uses a new ID system, the cat13 ID (spelled in lowercase this time) is instead given to Stinky (whose ID was CAT8 in the N64 and GameCube installments).
• An ID for a scrapped bear villager, BEA3. No additional data is present in the leaked files, with their associated folder being completely absent, and no villagers in Animal Crossing reuse their ID.

The choice to include a train as the primary mode of transportation was inspired by a book Eiji Aonuma read to his son, "The Tracks Go On" by Fumiko Takeshita and Mamoru Suzuki. In this book, children lay down tracks for a train as it progresses across the countryside. A year of the game's two-year development time was spent working on the ability to lay down tracks before the feature was ultimately cut.

Kaito, Sugiura, and Makoto from the Judgment sub-series make cameo appearances in the games Like a Dragon Gaiden: The Man Who Erased His Name, and Like a Dragon: Infinite Wealth. Despite this, Judgment's main protagonist Takayuki Yagami has never made a cameo in the Yakuza series. This may be due to the fact that his face was modeled after his voice actor, Takuya Kimura, who is a popular celebrity in Japan and could be expensive to license out.

In certain scenes in Portal 2, the player is required to quickly place a portal to get out of a dangerous situation. According to developer Dave Saunders, during playtesting, it was noticed that lots of players were dying during these segments because they placed the wrong color portals, so the developers specifically changed it so that clicking any button will result in the correct colored portal.

In Episode 5, on the second floor of the bookstore, a poster can be found on a wall reading "How to catch the legendary Dopefish", featuring an image of the Dopefish from Commander Keen: Goodbye Galaxy!, who has made cameo appearances in many other games since his first appearance.