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.

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.

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.

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.

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.