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.

Both the original GameCube release and the Nintendo Switch remake are rated E by the Entertainment Software Ratings Board (ESRB), but the GameCube version's rating was simply given the descriptor "Mild Cartoon Violence". The remake’s ESRB rating was updated to replace it with the descriptors "Mild Fantasy Violence" and "Mild Suggestive Themes". These "Mild Suggestive Themes" most likely refer to flirtatious dialogue (i.e. "Aren’t you a fine specimen of a man"; "Perhaps if I…grabbed you and gave you a little sugar") and a character with a large chest/exaggerated proportions, referencing Madame Flurrie.

Winning the in-game Happy Lucky Lottery isn't actually based on luck at all, but on the date from when you bought the ticket based off of the GameCube's internal clock. The prizes are as follow: 4th prize is anywhere between 4 to 10 days, 3rd prize is 25 to 35 days, 2nd prize is 85 to 115 days, and 1st prize is 335 to 395 days. If you change the system's clock to a day prior and went back to talk to Lucky who runs the lottery, he'll know that the internal clock has been messed with. You can either admit to it or lie to not having tampered with it, however you'll need to pay 500 coins in order to reset the lottery, regardless. Daylight savings is not put into account. Buying a new ticket won't actually increase your chances of winning either but will instead reset the days back to 0 from when you bought it.

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.

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.

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

There are a series of glitches that will lead to the character Flavio joining Mario's party and never leaving. He will also appear in cutscenes that Mario himself is not even in.

Francesca's name in the Italian translation of the game, Romoletta, paired with Frankie's translated name, Giuliano, makes a reference to Romeo and Juliet, whose love is impossible due to their families rivalry. The name Francesca can also be considered the female counterpart of Frankie, underlining their link.

It's impossible to lose the first battle in the game to Lord Crump. Even if the player enters the fight with only 1 HP due to taking damage from environmental hazards, the game will increase the player's health to five at the start of the fight and only allow the player to attack or defend.

Early designs for Smorgs can be found in the game's files. They look less fuzzy than in their final design.

The ringtone when Peach calls Mario is the title screen music from Super Mario World.

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.