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

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.

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.

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.

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.

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.

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.

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

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 ).

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.

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.

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.

An early Bonetail texture can be found in the game's data. The only difference is that it has a blue eye. In the final game, Bonetail doesn't have a visible eye, only empty sockets.

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

An earlier version of Mario can be found in the game's files. This version has a thinner outline, much softer colors, and a black moustache. This unused design looks similar to his appearance in the original Paper Mario.