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.

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 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 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 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.

There are multiple linked graffiti shapes found throughout the game that when sprayed will spawn a Blue Coin at the opposing linked shape location. If the player talks to an NPC on the same frame that the graffiti is fully cleaned, the game will become unplayable.

In Episode 6 of Bianco Hills, the sun in the sky is not present. This may have been an oversight by the developers since the sun is a separate object and not part of the game's skybox.

In the opening cutscene, an error can be seen in the Isle Delfino advertisement video. The image for Bianco Hills features Mario in the bottom-right corner.

Many locations in Isle Delfino feature a series of swirl-shaped glyphs. While seemingly unreadable to the average player, these symbols are actually a cipher for the Latin alphabet. Consequently, most instances of them can be decoded to generate coherent messages:

• The sign on the Sand Cabana in Gelato Beach reads "BAR GELATO".
• The sign above the entrance to Pinna Park reads "PARCO", the Italian word for "park."
• The sign on Pinna Park's pendulum ships ride reads "VIKING".
• The Isle Delfino guide book's preview image for Noki Bay features symbols in the corners that read "NOKI" when read in the following order: top-left, top-right, bottom-left, and bottom-right.
• The flag atop the orange dome in Noki Bay reads "MARE VILLAGE", the location's Japanese name.

In some instances, however, the translation does not produce actual words or sentences:

• The wall paintings throughout Noki Bay feature various nonsense combinations of letters, with some featuring just one.
• The stone trimmings in various parts of Noki Bay simply repeat the alphabet from A to Z.
• In the international release, the game's signboards read "RZTU BOD TVR". Of note is that this is a replacement for English placeholder text that was featured in the Japanese version. The placeholder text is taken from a dictionary, with some portions inexplicably removed. The unaltered text reads "This isn't gonna hurt a bit. Just a little stick. Ready? 1...2...3. There you go. All done," while the text that appears in-game reads "This isn't gonna Just a little stick. Ready? 1...2...3. There you All do."

In Pinna Park, if you lure a Strollin' Stu to the edge of the water fountain facing a pair of large, pink Bowser Jr. balloons, then flip over the Stu with a spray, it can be slung at the lower Bowser Jr. balloon, popping it. Normally, it was previously believed that these could only be popped using the water rockets during the rollercoaster minigames in Episodes 1 & 8. If the player pops this balloon and then triggers the rollercoaster event, the balloon will appear to respawn. In reality, the balloons on the overworld and the balloons in the minigame are different and placed in slightly different spots each.

An unused Goop effect can be found in the game's files that, when Mario jumps into it, will cause him to sink like it was quicksand and take damage. This effect causes Mario to perform unique struggling animations and voice clips that are not found anywhere in the final game, suggesting that this Goop variant was cut late into development.

Eely-Mouth, the giant eel boss in Noki City, has an esophagus and stomach modeled with a significant amount of polygons. However, the game's camera never travels inside the eel at any point during the boss battle, leaving its detailed innards unseen during normal gameplay.

At one point in development, Pinna Park was meant to function as another hub area. This is evidenced by the fact there are four unused "gate" objects found in the stage's files. These include a ring of manta rays, a shell containing a portal to Noki Bay, and a portal that goes to Pianta Village. The stage also has a MarioPositionObj, which controls where Mario ends up after leaving a course. The only other stage in the game that has gates and MarioPosition objects is Delfino Plaza.

During the game's opening cut scene, multiple cuts of Peach on the airstrip seem to have an error where the texture for her earrings use the texture for her eyes. This mistake is seemingly fixed from her first close-up onward.

In the Japanese version, Isle Delfino is named Dolphic Island. However, both the English and Japanese release use the same English voice acting, so in the in-flight infomercial still mentions Isle Delfino in the Japanese version.

In Episode 6 of Sirena Beach, the US version requires player to clean up about 95% of the goo littering the level in order to complete it. In the Japanese version, the player is required to clean up about 99% of the goo.

In the Japanese version, the name of some levels a different compared to the US version.

• US: Pianta Village - Japan: Monte Village
• US: Gelato Beach - Japan: Mamma Beach
• US: Noki Bay - Japan: Mare Bay

The messages that appear when you lose a life in Super Mario Sunshine and Super Mario Galaxy differ between regional releases of the games. In the Japanese versions of both Sunshine and Galaxy, when you lose a life the text says "Miss!", but this was changed in the international versions of the games to say "Too bad!". The only difference is the Korean version of Galaxy, where the text was reverted back to "Miss!"

During the development of Super Mario Sunshine, the team planned for a multiplayer mode. One player would play as Mario and the other would play as Shadow Mario. When the players moved away from each other the camera would move out. There was even a function in the game's code to determine if a map belonged to the multiplayer mode of the game, entitled "SMS_isMultiplayerMap".

There is an unused enemy named "Kug" found in the games files. Although there's no way to access it normally, it can be found under Pinna Park by glitching the camera, or by using a cheat device.