In Episode 7 of Sirena Beach, if the player defeats Shadow Mario on the staircase inside of the Hotel Delfino, the Shine Sprite will become bugged, and when grabbed Mario will clip into the stairs. You are still able to exit the level through the menu, but your progress will be lost in the level.

In Episode 8 of Ricco Harbor, a secret 1-Up Mushroom can be obtained through an obscure set of interactions with three duck intertube-riding Piantas. Since they are not interactable while in the water, it is only possible to interact with them by waiting long enough at certain low areas by the water. Once all three Piantas have been talked to, the last one you speak to will reward you with a 1-Up at the starting location of the episode.

In the seventh episode of each course, the player is required to chase down and defeat Shadow Mario to obtain a Shine Sprite, which spawns from his dematerializing body as he teleports away. In actuality, the Shine Sprites are stored at fixed locations and are simply teleported to his location by the flag "appearShineFromKageMario". If the flag is replaced with "appearShineFromNPC", the Shine Sprites appear where they are stored, implying that these were their originally intended locations. The fixed points in "Shadow Mario Revisited", "Hold It, Shadow Mario!", and "Shadow Mario Runs Wild" also feature dedicated cameras for spawning cutscenes, corroborating the idea.

Of note is that the internal location for the Shine Sprite in "Shadow Mario Runs Wild" places it partially inside Pianta Village's golden mushroom, which further implies that this object had its height raised at some point during development.

In a 2002 staff interview with Nintendo Dream, director Yoshiaki Koizumi revealed that FLUDD was inspired by his memories of playing with water guns as a kid, an image that he recalled upon first using the analog L & R triggers on the GameCube's controller. Series creator Shigeru Miyamoto further explained that the concept behind FLUDD was controversial among Nintendo's staff due to Mario not being widely associated with these kinds of tools, though Luigi's use of the Poltergust in Luigi's Mansion ultimately served as a precedent in the concept's favor.

In the same interview, Takashi Tezuka stated that Nintendo went to great lengths to keep FLUDD from resembling a firearm, both due to Koizumi finding a water gun "too simple" and due to concerns that guns (or anything that audiences may interpret as such) would be inappropriate for the franchise's public image. The "weird backpack thing" that FLUDD ultimately ended up as addressed both concerns at once, with Koizumi likening it to firefighting equipment and "a [plastic] bottle water rocket toy."

In a 2002 developer interview archived by the now-defunct blog GSLA, director Yoshiaki Koizumi revealed that the game's staff originally came up with ten different nozzles for FLUDD, devising new ones for each possible situation Mario might encounter. However, this was reduced to three to avoid similarities to the gameplay style of The Legend of Zelda series. Some remnants of this larger quantity can be found in the final game's data, which includes an unused model for a Yoshi head nozzle and parameters for a sniper nozzle. While the former's properties are unknown beyond its appearance (with its model lacking any associated animations), the latter would have been 100 times more powerful than the Squirt Nozzle and would've had a significantly larger hitbox. However, it also would've required Mario to charge it like the Rocket Nozzle and Turbo Nozzle.