The "Ok desu ka" that sounds on the Character Naming screen is voiced by Shigesato Itoi, who was tricked into saying it into a hidden tape recorder by Hirokazu Tanaka, the music composer for the Mother 1 and Mother 2.

In Chapter 7, when a hooded Mr. Saturn gives you back the Courage Badge, he says goodbye to the player and walks a few spaces offscreen where it is supposed to stop and disappear. However, due to a bug, he remains in that spot, just a few spaces away from the player. Itoi liked this bug, so he decided to keep it there and write some text for him.

Mother 3 was originally going to be a 3D game for the Nintendo 64 DD add-on. Dubbed "Earthbound 64" by fans, the game was delayed several times due to the little experience the development team had with 3D games. The game would have possibly utilized the N64 DD's features and would also possibly use Mario Artist to create new in-game character faces. The Rumble Pak was also considered to be used during battle sequences. Due to the commercial failure of the N64 DD, the game was canceled but later recreated for the Game Boy Advance.

On February 9, 2007, nearly a year after the game's release, director and series creator Shigesato Itoi set up an online quiz for fans who had completed the game, testing their knowledge about it. One question asks which Thief Jujitsu technique Wess uses, with the options being:

• "Super Sunset Miracle Chop Again"
• "Super Chop Miracle Sunset Again"
• "Super Miracle Sunset Chop Again"
• "Miracle Chop Super Sunset Again"
• "Miracle Chop Super Sunrise Again"
• "Miracle Sunset Super Chop Again"

None of this corresponds with anything seen in the final game, and a note attached to the question clarifies that it was based on something that was removed during development, telling fans to ignore it. Because the intended answer was never confirmed by anyone on the Mother 3 development team, it is unknown what the true name of the technique was. Similarly, the question doesn't clarify what the technique would've been used for, though the phrase "Thief Jujitsu" is most similar to the Secret Thief Arts Technique that Wess occasionally uses in battle.

In an interview with Nintendo Dream conducted roughly three months after the release of Mother 3, director and series creator Shigesato Itoi stated that the Magypsies were designed as a deliberate contrast with the game's otherwise "macho" setting. Rather than responding to violence with violence, they intervene through peaceful means and live fully aware of and comfortable with the inevitability of death.

In the same interview, Itoi also stated that he made representation a big part of the game's cast: the Magypsies were inspired by friends of his (though he did not specify if this referred to their philosophies or their depiction as nonbinary figures who take after drag culture), and Duster was given a limp "because there are handicapped people in our world." According to Itoi, the idea behind this was to encourage an anti-discrimination message.