While developing the plot for Batman: Arkham Knight, Warner Bros. Games concluded from a ratings analysis that certain scenes would cause "issues", so they requested a Mature rating from the Entertainment Software Ratings Board. Rocksteady Games founder Sefton Hill was initially surprised and scared by this, as the game didn't include "gratuitous blood or swearing" and he believed the rating would take away the team's creative freedom. After a phone call with WB Games' vice president of production Ames Kirshen calmed these fears, Hill agreed to go forward with the M rating.

The rating was likely triggered by scenes such as the player as Batman interrogating a Militia grunt by using the wheel of the Batmoblie to torture him for information, the Professor Pyg sequence with blood being splattered all over the room, and unarmed characters being shot in cutscenes and while playing as Spoiler:the Joker. Hill was aware that this meant certain people would not be able to play the game, but he stated that he didn't want to compromise any of the game's content despite not writing the game with that rating in mind.

A random encounter that one may come across is a pipe sticking up out of the ground emitting a gas with a corpse holding a note that reads: "PIPE IS LIFE". This was originally a joke idea that level designer Zachary Wilson proudly put in as "some nonsense [he] made at 8PM on a Wednesday at the end of the project when no one was looking."

According to planner Atsushi Tomita, the team originally planned for the final boss Apocalypse to be human-sized, but eventually decided against it due to the lackluster reaction to Thanos as a boss in the previous game, and because of the effort and memory capacity it would take to create. Instead, they decided to make him huge to save on space (by giving him minimalistic animations) and to surprise fans. The freed up space was used to add Cammy into the game.

In November 2005, the watchdog advocacy group MediaWise (controlled by the National Institute on Media and the Family) joined by United States senator Joe Lieberman published their annual report on offensive content in video games. At the press conference to present their findings, they highlighted games featuring cannibalism, and particularly criticized F.E.A.R. and Stubbs the Zombie in Rebel Without a Pulse as games to avoid out of concern that they would be harmful to young children, despite the games being aimed at a mature audience. Developer Wideload Games fired back with a humorous response claiming the watchdog group was arguing semantics, as Stubbs ate brains not because he was a cannibal in the vein of a serial killer, but because: "Stubbs is a zombie. [...] Zombies eat brains. That's what they do."

The African Kingdoms expansion added to Age of Empires II: HD Edition in 2015 would draw ire from some fans due to the inclusion of the Portuguese as one of the four new civilizations, as Portugal was not an African civilization, but European. This culminated in the creation of "Alberto Barbosa", a meme originating from 4chan's international imageboard which took artwork of an African man on the expansion's cover art and edited the modern-day flag of Portugal over his turban.

Of the original 13 civilizations featured in the game, only the Britons completely lacked any gunpowder units or Bombard Towers. However, they would quickly be joined by the Aztecs and Mayans, which were introduced in The Conquerors expansion pack in 2000.

In a pre-release interview with director Bruce Shelley, he described how a civilization's distinct bonuses helped differentiate them, specifically citing that Shang villagers moved faster. However, in the final release of the game, this bonus was instead given to the Assyrians and Yamato. The Shang bonuses would instead turn out to be cheaper Villagers and more HP for their walls.

Following the release of the Game Boy Advance port of Aero the Acro-Bat in 2002, series creator David Siller expressed interest in bringing the other two games in the series, Aero the Acro-Bat 2 and Zero the Kamikaze Squirrel, to the handheld, possibly in a single collection called the "A-Z Force". However, these ports would never be released.

Mandy's ultimate attack, in which she smiles at her opponents and causes them to explode, is a reference to the season 5 episode "My Fair Mandy". In this episode, it is revealed that whenever Mandy smiles it leads to cataclysmic events.

The Italian mobsters operating in the Buca De Faggoncini are an obvious homage to the cast of the 1999 TV series "The Sopranos", specifically Tony Soprano, Christopher Moltisanti, Salvatore "Big Pussy" Bonpensiero, Silvio Dante and Paulie Gualtieri. Classi at one point even describes them as "Tony Soprano-looking motherfuckers".

The longtime fan term "Eeveelution", which refers to the various evolutions of the Pokémon Eevee, first appeared in the 2001 Nintendo Power Player's Guide for Pokémon Stadium 2. It was first used within an official game in 2008's Pokémon Ranger: Shadows of Almia.

The American release of Pokémon Stadium 2 has a two-toned cartridge, with the front being gold-colored and the back being silver-colored in line with the background of the game's box art. This is a reference to Pokémon Gold and Pokémon Silver, which could transfer information to the game using the Nintendo 64 Transfer Pak.

The American release of the game has an exclusive spelling error, where two Ninetales cards are mistakenly spelled "Ninetails." However, Ninetales is spelled correctly in one of the cards' description texts. This was fixed in the European release.

Within the data of Chapters 2, 3, and 4 is a variable for the TP meter titled "shit," which is set to 1 whenever the global.tensionselect variable (used to indicate the amount of TP required to cast the currently selected spell) is uninitialized. Under these conditions, the game is programmed to play the recurring splat soundbyte. In Chapter 5, this variable is renamed "toylet." The purpose behind this variable is to bypass an issue where Game Maker crashes when trying to call a variable that hasn't been initialized yet; consequently, the "shit"/"toylet" variable serves as a means of highlighting such errors without disrupting gameplay.

General Skarr's gardener alternate costume is based upon his design from the season 5 episode "Herbicidal Maniac", while his default appearance is based upon his original design from Evil Con Carne, the sister series to The Grim Adventures of Billy & Mandy, where he originated.

Shinobu Kamizono's model from Gal*Gun: Double Peace can be found within the game files, likely having been ported over for testing purposes. Comparing it to her model in Gal*Gun 2 reveals various subtle changes made to the character models in the game:

• Due to shoes now being treated as a separate piece of clothing, the "Body" models are now barefoot by default.
• Skirts and ties were made looser in order to show off the cloth physics.
• "Face" models are simplified, being flatter and smoother with rounder ears.
• The overall polycount of the models are generally lower than before.

The first puzzle to be implemented into the game involved a scenario where one player had to walk through a tunnel while the other player opened doors to let the player in the tunnel through. According to co-designer Jacob Strasser, this was later removed from the game after the developers decided that the puzzle was "un-fun".