Mother 3+, the game's physical soundtrack, contains a remix of Big Shot's theme. This remix is heavily based on the theme used in the trailer for Earthbound/Mother 64. The track's name, "A Great Person Theme", instead of "Big Shot's Theme", suggests that this particular version of the song was created earlier in the game's development, possibly when it was still planned to be a 64DD game.

In Chapter 2, during the cutscene just before Kumatora joins the party as a permanent member, she fires PK Freeze α at Duster and Wess when they walk into the stairwell she was in, not immediately recognizing who they were. PK Freeze α costs 5 PP to use. After the cutscene ends, if you check Kumatora's status, she will have 68 PP out of 73 PP remaining.

This detail could imply one of two things:
•She had her Magic Pendant equipped increasing her Maximum PP by 5 but not increasing the Total PP she already had and that the cutscene's use of PK Freeze α did nothing.
OR
•She did start with 73 PP without the Magic Pendant being equipped and her use of PK Freeze α during the cutscene actually did drain her Total PP by 5.

Regardless of which option was intended, both still imply that for whatever reason, the developers had the foresight to have Kumatora join the party without having a full PP meter.

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.

After the three-year time skip in the game's story, Lucas and Fuel each receive a new set of sprites showing that they went through an obvious growth spurt in that time. This is most easily distinguished by the size of their bodies and heads, where young Lucas and Fuel are scrunched down compared to their older selves. Kumatora also receives a new set of sprites after the time skip, but her growth spurt is less obvious since she was already a teenager with a tall body and head before the time skip. Aside from some additional cyan streaks on her hoodie, the only detail indicating she physically aged after the time skip is that her legs are one pixel taller.

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.