In the Japanese version, Oil Man had black skin with peach-colored lips.
In the US/European versions, he was recolored blue with yellow lips.

Defeating an enemy with a non-buster weapon in the Japanese version of the Mega Man Zero series would make robot characters spout out something resembling blood. It was removed in the US/European versions. Oddly enough, the rating for the Japanese version of the Mega Man Zero series were unaffected.

The music that plays in the opening is different in the American Release than in the Japanese release.

There is a glitch in the PAL version, that is not present in the American/Japanese versions.

Finishing a mission between 00'50"00-00'59"99 and 01'50"00-01'59"99, removes 50 seconds from the timer, giving the player an impression that they finished the mission faster.

There was originally going to be a Sphinx themed mini-boss in Pharaoh Man's stage. It was functional in some demo versions of the game, but the Sphinx is not present in the final release.

In an interview with GameInformer, Dave Mervik stated that the short length of the game was intentional, as it was the developers’ first original title and they wanted to emphasize quality over quantity.

The idea to develop the game as an MMORPG was conceived by executive producer Hironobu Sakaguchi when he was impressed by western MMOs, such as EverQuest. He convinced Square to begin the development of their own online game, suggesting that it be based on the Final Fantasy series.

The Bokujō Monogatari series, as it's originally known in Japan, which translates to "Farm Story", was known in the West as Harvest Moon up until 2014 where it was changed to Story of Seasons. This was because Western localization of the series was handed over to XSEED, a subsidiary of Marvelous AQL who owns Bokujō Monogatari, instead of to Natsume, who had been localizing the series in the West since the very first title. Because Natsume owned the trademark for Harvest Moon and not Marvellous, Natsume decided to create their own series of original games under the Harvest Moon name, prompting XSEED to rename the Bokujō Monogatari series in the West to Story of Seasons.

Ninja theory originally signed a deal with Green Screen to publish the game, however, Green Screen went out of business a month later, resulting in Bandai Namco picking up the title.

The Cold War setting was chosen, because Director Hal Barwood felt that nazis were used too often in Indiana Jones properties, and a change of setting would benefit the title.

If you enter the password "CHEESE!!" on the Nintendo 64 version, you'll see a photo of LucasArts' Developers.

There is a drawing of what appears to be an early loading screen left in the PlayStation 2 version's data.

The main inspiration for the game's story was the Bankruptcy of Lehman Brothers in 2008; the largest bankruptcy filing in U.S. history.

The 8-bit graphics were designed to appear "old-school", resembling 8-bit RPGs such as early Dragon Quest and Final Fantasy games, and make the player use their imagination.

During a Square Enix Presents segment at E3 2015, Tetsuya Nomura revealed that the kingdom of Corona from Tangled was one of the first worlds to be considered for the game.

The ball-shaped planet in the 3D special stage was based on King Kai's Planet from the Dragon Ball anime series.

In Neverland, there's an unused room that only has a skybox of the night sky.

In the Japanese version version of the game, it's only possible to earn Mission Crowns by playing the game's Mission Mode in multiplayer, but in the western versions, the player can be awarded crowns in both single player and multiplayer modes.

In the western versions of the game, the mission mode difficulty was toned down. As a result of that, enemies are given less HP, the player is awarded Munny for beating missions, and some of the enemies enemies take less damage than they do in the Japanese version.

A placeholder logo for a company called "Light & Shadow Production" can be found in the PlayStation 2 version's data.