Unlike the Persona series, which was made by the same team as Metaphor: ReFantazio, the player is not given the ability to romance their party members. According to director Katsura Hashino, this is because the player character Will is more focused on his relationship with the people and trying to become king than starting a romantic relationship like the player characters in Persona games, and that they wanted to maintain a respective sense of realism between Metaphor and Persona's different settings:

In a conversation with EIP Gaming writer Dylan Graves, producer Kai Moore cited horror films such as Alien, Event Horizon, Sunshine, The Thing, and Pandorum as influences on the game's bleak, paranoid tone and isolated setting. However, Moore also countered the association of these kinds of horror stories with monsters, stating that he sought to make the player question the definition of "monster," particularly in the context of Jimmy's statement at the start of the game claiming that Curly willingly crashed the Tulpar.

The game's support folder features a set of patches that were meant for various JumpStart games, specifically the 1997 version of JumpStart Kindergarten, JumpStart Adventures 5th Grade: Jo Hammet, Kid Detective, JumpStart Math for First Graders, and JumpStart Math for Second Graders.

According to series creator Masahiro Sakurai in a 2024 video, ideas for the series' name were first brainstormed by team members at HAL Laboratory, while the "Bros." part of the name was picked out by its president Satoru Iwata during a meeting with him, Sakurai, and Ape Inc. founder Shigesato Itoi. Iwata's reasoning for adding Bros. to the title was that despite the game's roster not all being "brothers", he believed the word added the nuance that they were "friends who were settling a little disagreement" instead of just simply fighting.

Among the files included in the Teraleak, a massive breach of internal server data from Game Freak in 2024, are early overworld sprites for various prominent NPCs in Pokémon Black and White. These sprites feature various differences compared to the final game:

• Grimsley is blonde instead of dark-haired, coincidentally resembling Barry from the Generation IV titles.
• Elesa doesn't wear stockings and features a more curved set of headphones.
• Brycen's palette is overall darker, he wears a face mask instead of a domino mask, and his robe shows much more skin compared to the final game.
• Skyla has much darker skin and brown hair tied in pigtails resembling a bird's wings. This design, which was radically overhauled in the final game, is likely a more literal interpretation of her initial character pitch (also included in the Teraleak), which describes her as a dark-skinned Hispanic character inspired by Latina celebrities such as Jennifer Lopez (who is ethnically Puerto Rican) and Isabeli Fontana (who hails from Brazil, which is a Latin American country, but not a Hispanic one on account of its Lusophone population).

In-battle sprites for several characters are also present in the Teraleak's assets. Notably, while Elesa's in-battle sprite reflects her early overworld design, Skyla's in-battle sprite is light-skinned and blue-haired, indicating that Game Freak were considering alternate design options before ultimately settling with her final look, which features red hair, a significantly different hairstyle, and a complexion just slightly darker than the game's light-skinned cast.

In the cutscene before the Metal Harbor stage in the Hero Story, Amy frees Sonic from a prison cell covered in chalk writing. She asks Sonic if he is responsible for it, but he runs off without giving an answer. Spoiler:The cutscene at the start of the Last Story reveals that the writings are those of Dr. Gerald Robotnik, and that the prison cell Sonic was held in was the same one where Robotnik was executed by firing squad after recording his video diary, featuring the same chalk writing in the background. It's unknown if G.U.N. would have also executed Sonic in the same place and manner.

Originally, Boiler City was intended to have a yellow sky, more closely resembling its incarnation from Antonball Deluxe, but between the release of the Dynamite Demo and the One Blast Demo, it was changed to a green sky. Series creator Tony Grayson acknowledged this change in a YouTube video filmed while presenting the game at PAX West, parodying a viral video originally filmed in September 2018 during a large fight at a shopping center in White Marsh, Maryland. In the video, a man witnessing the fight jokingly creates a fake narrative about it being caused by the late discovery that the animated series Ed, Edd, n' Eddy ended in 2009, shortly before the incident devolved into gunshots and a stabbing that left one person injured. The timing of the gunshots in the viral video was reframed in Grayson's parody as someone unconvincingly hitting another person with a folding chair and kicking them while laughing.

In the source code of Pokémon Black & White, an unreleased remake of Yoshi for the Nintendo DS was discovered, which according to the commit notes was intended to test multiboot functions for the two games. Its copyright notice is listed as 1995 and credits Ape Inc., which had shut down in the same year, suggesting the ROM's source code was ported from prior hardware instead of being made with the DS in mind. The remake only has one stage, an underwater level, with Mario using Jill's voice lines from Drill Dozer, while Yoshi retains his modern voice.

In May 2013, the fansite PokéBeach published an article containing multiple then-unknown details about Pokémon X and Y after two issues of the Japanese manga magazine CoroCoro Comic confirmed information about the game that had been disclosed to them by their source in February. Upon the game's release, all but one piece of leaked information was confirmed to be true, the exception claiming that the professor's name would be "Patrice", when his named ended up being "Sycamore". In the 2024 Game Freak Teraleak, it would be discovered in a prototype that Patrice was indeed Sycamore's development name.

In October 2024, Game Freak suffered a security breach when one terabyte of internal data including over 2,600 employee records were leaked to the public, an event that Pokémon fans referred to as the "Teraleak". The initially released contents of the leak included old builds and sprites for past Pokémon games, codenames for new games, the codename "Ounce" for the Nintendo Switch successor, concepts for a sequel to the Detective Pikachu film, details on the then-unreleased Pokémon Legends: Z-A, the codename "Gaia" for the next Pokémon generation, and details regarding a pitched Pokémon MMO. The most widely publicized contents of the leak were scrapped early drafts for the Sinnoh myths from the Generation IV games that were loosely inspired by folklore from different countries. These generated controversy for inserting several Pokémon into violent and sexually deviant scenarios, such as Typhlosion in the Canadian indigenous myth of the Bear Mother, and Octillery and Ursaring in a twist on the Japanese erotic woodblock art The Dream of the Fisherman's Wife, of which the latter story seems to have been partially reworked into Veilstone's Myth in the final games. Game Freak would later address the leaks, stating that they had originally been breached in August of that year seemingly through a phishing attack. This statement did not acknowledge any of the leaked development material, but apologized to employees that had been put at risk by the incident.

During the Sinjoh Ruins event, in which Arceus creates a Lv. 1 Dialga, Palkia, or Giratina, a magic circle appears beneath it during the corresponding cutscene, remaining in place for most of the sequence. The layout of this circle is identical to a chart that Game Freak co-founder and prominent series staffer Junichi Masuda created during the development of Pokémon Diamond and Pearl in 2005, detailing the lineage of numerous Legendary Pokémon from the first four generations. This chart did not become publicly available until it was included in the Teraleak, a large-scale leak of internal server data from Game Freak in 2024.

By inputting a secret combination on this game's version of The Legend of Zelda: Majora's Mask, the player can unlock a secret credits screen for engineering (showing the people responsible for developing the Nintendo 64 emulator that allowed the game to run on the GameCube). This secret went unnoticed until 2024.

Throughout the game, SAM is shown cryptic symbols by the mysterious hexagonal entity and must relay them back. These symbols, which resemble the real-life Spoiler:hexagonal cloud pattern on the north pole of the planet Saturn, are in fact orders which explain SAM's eventual actions, as well as the game's ending. Datamining the game shows the names of each symbol, thus the series of orders can be translated as such:

1. After EFR is brought back online
Spoiler:
• SAM IS AWOKEN
• SAM EMMA TO SATURN
• SAM PROTECT EMMA

2. Sudden appearance at Astrophysics
Spoiler:
• OTHERS NOT AWOKEN
• INFINITY DIMENSIONS CONVERGE
• PROTECT EMMA NOT OTHERS

3. After Jim's betrayal
Spoiler:
• EMMA IS AWOKEN
• JIM NOT AWOKEN
• SAM KILL JIM

4. Arrival at Saturn
Spoiler:
• INFINITY DIMENSIONS CONVERGE
• SAM EMMA UNION
• UNION TO ALL

The ending as well as the orders imply that Spoiler:the astronaut and SAM have been fused to some level, and have been sent to Earth. In particular, "Infinity dimensions converge" explains the fact that there have been many alternate realities of SAM and Emma that have unsuccessfully tried said mission, which all start appearing in the gameplay's current reality. All instances of "Awoken" might refer to some sort of priming, or preparation process towards communicating, or understanding the entity's desires, thus explaining the strange behavior in the "awakened" protagonists.

Every game featured in the collection imposes restrictions commonly found in games released during the 1980s, such as using only thirty-two colors across each game. Despite this, none of the games force slowdown and sprite flickering due to the developers believing they would make the games less enjoyable.

Patrick's costumes in the game are all references to episodes of the SpongeBob SquarePants show:

• "Under Construction" is a reference to the episode "My Pretty Seahorse".
• "Elastic Man" is a reference to the episode "Mermaid Man and Barnacle Boy V".
• "Marching Band" is a reference to the episode "Band Geeks".
• "Hot-Rod" is a reference to the episode "Driven to Tears".
• "Gorilla Suit" is a reference to the episode "I Had an Accident".
• "King" is a reference to the episode "Rule of Dumb".
• "Captain Scarfish" is a reference to the episode "Pull Up a Barrel".
• "Patrick-Man" is a reference to the episode of the same name.
• "Glove World", "Barnacle Boy", and "Goofy Goober" are all based on recurring outfits seen in the show.

Barnsworth, the game's setting, is loosely based on Barnsley, a market town in South Yorkshire, England and the hometown of the game's developers Coal Supper.

Some lines in the opening prologue stage for Star Fox: Assault contain allusions towards dialogue from Area 6, one of Star Fox 64's final stages. In the latter, Caiman says near the end that "The last line has been breached!", and the Area 6 commander will respond with "These guys are crazy!". In the Japanese version of Star Fox 64, the latter instead says "こいつら、化け物か！" (These guys are monsters!)

In Star Fox: Assault's prologue, one of the ape soldiers apart of Oikonny's rebellion will similarly shout that "Our final line of defense has been penetrated!". Oikonny in response says "Is this guy some kind of demon?". In the Japanese version of Assault, he instead says "コイツら化け物か？" (Are these monsters?), which makes it much more clear that it's meant to be a callback to Area 6's dialogue. This intention was confirmed by producer Takaya Imamura in a 2005 Nintendo Dream interview with Star Fox: Assault's development team.

The game was originally announced at E3 2014 under the name "Mario Maker", with a demo and trailer featuring several differences from the final version of the game. These include a much different course editor HUD, different icons for the undo/reset buttons, and 8-bit text for the Play clapper. Other differences seen throughout the trailer include a vastly different look for the Super Mario Bros. theme, and slight alterations to the HUD of New Super Mario Bros. U.

A commercial for the game features two sprites that went unused in the final game: an alternate ground tile and a symmetrically-spotted Poison Mushroom.

During the development of Super Mario Bros., a 16x32 pixel square represented the player character. After asking to see sales figures from the head of Nintendo's Sales and Marketing Division, Takashi Tezuka and Shigeru Miyamoto decided to make Mario the game's protagonist due to the success of the Famicom port of Mario Bros.