The gender identity of the party member Vivian is inconsistent between different language translations of the original game. In the Japanese version, Vivian identifies and presents as female, but is described by other characters in the game as actually being an effeminate-looking male, aligning with common media depictions of transgender or gender non-conforming characters at the time, but not explicitly referring to Vivian as such. A rough translation of the Japanese text for Vivian as a party member reads:


The French version directly carries this over and additionally describes Vivian as a boy pretending to be a girl, while the Spanish version describes Vivian as a boy who looks like a girl. However, according to former Nintendo of Europe translator Pol Roca, Vivian's Spanish name "Bibiana" was intended to be a reference to the Spanish transgender actress Bibiana Fernández, who starred in the 1977 film Cambio de Sexo (or Sex Change).

The English and German versions remove any references to being transgender or gender non-conforming, implicitly portraying Vivian as a cisgender woman with "a bit of an inferiority complex". Instead of being bullied over her biological sex, her sisters instead belittle her for her appearance.

The Italian version of the game on the other hand explicitly depicts Vivian as an openly proud transgender woman, with the localization reconfiguring her relationships with gender identity and her sisters by having Marilyn and Bedlam's bullying being rooted in jealousy, traits which are absent in the Japanese script:


The English release of the Nintendo Switch remake follows the Italian version of the original game in unambiguously describing Vivian as a transgender woman, most prominently featuring a line where Vivian states that "it took me a while to realize that I was [Marilyn and Beldam's] sister... not their brother." It's currently unknown if Vivian's portrayal in other translations of the remake has changed from the original release.

After Paper Mario: The Thousand-Year Door's announcement in 2003, some Mario fans incorrectly believed that the character of Madame Flurrie was going to be the ghost of Bowser's wife, based off of her character design and Japanese name. This is due to Flurrie's Japanese name, "Cloudia", sounding a lot like "Clawdia", a popular urban legend name for the Koopalings' mother supposedly created by the Mario fan website "Lemmy's Land", as well as Flurrie sharing a hair style with Ludwig and lip-shape with Wendy, who were at the time considered Bowser's children by Nintendo.

On June 12, 2008, the film studio Morgan Creek Productions filed a lawsuit against Nintendo of America, alleging that Hans Zimmer's song "You're So Cool" from the 1993 film "True Romance" was used in a commercial for Paper Mario: The Thousand-Year Door without permission.

Six days later, Morgan Creek dropped the lawsuit without comment. Nintendo would later release a statement revealing that the day before the lawsuit was dropped, Leo Burnett, their advertising agent, gave Morgan Creek "a copy of a music license entered into between Leo Burnett USA, on behalf of Nintendo of America and Morgan Creek, for licensing of the song."

At one point, the W Emblem was going to be purple. This would imply that when Mario equips the W Emblem, it was originally going to make Mario’s clothes transform into Waluigi’s clothes, as opposed to this happening by equipping the L and W Emblems in the final game.

Within the GameCube version's data are graphics for an earlier Vivian design depicting her with a shorter body and a flame on the tip of her hat. Concept art included in the Nintendo Switch remake reveals that the latter trait was part of an early design for all three Shadow Sirens, with Beldam and Marilyn also having a shard of ice and a lightning bolt at the end of their respective hats. This concept art additionally depicts the Shadow Sirens with black skin, which was changed to purple by the time the early Vivian sprite was created.

Despite Heff T. claiming that he can't get out of his own cabin, he can in fact be seen twice not within it.

An unused badge named "Trade Off" still exists in the games data. It was very close to being completed, but never saw the light of day. It had its name translated, and works properly. When used in battle, it will say "Rank Up." The player would be rewarded with more star points after the battle, but the enemies would become tougher.

In the Japanese version, Mario and his partners only get fully healed after completing Chapter 1, but they do not get healed at all after completing any of the other chapters. In the international version, Mario and his partners get fully healed for all of the chapters (besides chapter 8) after they are completed.

There are many unused songs and jingles in the game's data. Unfortunately, only two are still on the disk; there are plenty of file names, but no actual tracks to accompany them.

When tattling a Bob-omb named Fred in Fahr Outpost, Goombella mentions that he isn't very freaky for a Fred. This is a possible reference to the character Freaky Fred from the cartoon Courage the Cowardly Dog.

Grodus' dialogue has an error within the game's script. If the player chooses "Don't attack", he will say "WORM! You dare defy me?!?", even though the player is doing what he said. Likewise, if the player chooses "Attack", Grodus simply tells Mario to stop his blubbering. The responses appear to be the wrong way round.

TEC is likely based on HAL 9000 from the movie 2001: A Space Odyssey. Unlike HAL, TEC isn't insane or malevolent. Another Mario series spoof of HAL was HAL 9001 from The Super Mario Bros. Super Show! live-action episode "9001: A Mario Odyssey."

The fact that Ghost T. resides in Room 004 is a reference to Japanese and Chinese culture in which the number four (四; Rōmaji: shi, Pinyin: sì) is regarded as unlucky, as it sounds similar to the word "death" (死; Rōmaji: shi, Pinyin: sǐ ).

Eddy the Mask's name may be based on Eddie the Head, the mascot of British heavy metal band Iron Maiden.

During the battle with Vivian, she can use Fiery Jinx when her HP is low. However, when Vivian joins Mario's party she has to be Super Ranked to learn that ability.

If the player looks through Professor Frankly's trash can after fighting the Shadow Sirens, they can find Vivian's Tattle, but not Marilyn's or Beldam's. This foreshadows that Vivian would join the party, rather than fight Mario again with the other sirens, as only Tattles of one-time enemies can be found in the trash.

The color of each of the Shadow Sirens' hats matches the type of their attacks. Beldam's hat is blue, and she has a "Blizzard" attack. Marilyn's hat is yellow, and she has a "Thunder" attack. Vivian's hat is red, and can use a variety of fire attacks as Mario's partner.

Two names, help_A_access, and help_door_access can be found in the game's files. It says "Hah! I'm not telling you my secrets at the show! Wait for the final version!" These were used as an E3 demo and can't be found in the Multi-Game Demo disc for the Gamecube.

The interior of Mario's house in the opening scene contains a full recreation of the bedroom as it was in Paper Mario, even though only the tiniest bit of it is visible in the opening, and this room is never seen outside of a cutscene.

Though the Excess Express Engineer's name is not known for sure, his autograph seems to read "Carl".