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.

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.

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 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.

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.

Mother 3's official soundtrack, Mother 3+, contains a remix of the song "Snowman". This remix was reused 2 years later for Super Smash Bros. Brawl. The 2 tracks are near identical, with the only major difference being the intro to the song. The Brawl version uses a choir for the beginning, while Mother 3+ uses a wind sound in its place. The Brawl version also adds a drumbeat to the song on its second loop.

The Game Boy Advance contains the original Game Boy and Game Boy Color's CPU, the LR35902, for backwards compatibility purposes. In Mother 3, the song "Porky's Porkies" uses only the original DMG processor, and the inside variation of "No Eating Crackers in the Cinema" also primarily uses it, though the latter also uses a sampled bass line.

Within the game's files is a low-quality picture of the Summit Inn Cafe, a famous roadside diner built on Route 66 in California. The image was most likely used for graphics testing, though it might have also been used as a reference for the Dur-T Cafe seen in Chapter 5.

The track "The Water's Great", that plays while in a hot spring, has the same melody as "Open Sesame Tofu", which plays during The Wess Dance to open a few doors in the game, but is much slower. Although The two pieces of music and the events they accompany seem to be completely unrelated.

In Chapter 8 during Leder's story, the music that plays, "Leder's Gymnopedie", is both named after and an adaptation of Erik Satie's "Gymnopedie No.1"

Shigesato Itoi stated in an interview that Tanetane Island and its hallucinations were based on his affinity for the television shows "Twin Peaks" and "Lost".

The enemy, Gently Weeping Guitar, is a reference to The Beatle's song, "While My Guitar Gently Weeps".

Claus has over 150 unused sprites, the most out of all the characters in the game, including full running and walking animations in a bathing suit.

There is an unused favorite food item that heals 300 HP to a single party member, which can be bought for 200 DP. Suggesting that the favorite food was planned for inclusion at some point of the game.

Footage of the game taken during its development period on the Nintendo 64DD shows Ness, the protagonist from Earthbound, to be a playable character. The footage shows Ness riding the Pork Bean through a desert area, as well as him running through a jungle.

When fighting Mr. Passion or Lord Passion, his background music contains samples from Famous Composers, such as Beethoven's Symphony No. 5 in C Minor and Tchaikovsky's Piano Concerto No. 1 in B flat Minor.

In one of the caves, a simplistic map of Japan can be seen on the floor.

Shigesato Itoi stated in an interview that, due to Porky's immortality, he will still be alive 5.5 billion years after the date at which the interview was taken, when the world has ended, stating that "the grief of that is incredibly depressing to me. It's amazing... Porky is truly a poem in himself.."

There are two inaccessible rooms in the Toilet Dungeon in Chapter 8: one where water seeps from the bottom of the door and another where a man rushes in and locks the door. By cheating, one can see what's inside these rooms, which is an overflowing toilet for the first and a bathroom full of toilet paper for the second.

Shogo Sakai was the only person in charge of all the music in Mother 3, which count up to being 250 songs. Itoi realized even before he started development that he couldn't just request an outside musician and wanted someone who would have a lot of time to work on the project.