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.

In the Japanese version, the texture for signposts uses English placeholder text 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." The international release replaces the text with a series of unreadable, swirl-shaped glyphs.

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

In the Japanese version, when you lose a life the text says "Miss!". In the international versions the text says "Too bad!".

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.

There's an unused sound file of Mario saying "Ciao", which was possibly meant to play when you start up the game.

In the Hotel Delfino stage's ventilation shaft, there's a janitor who says "All these ghosts are causing such trouble... They're everywhere! Why can't someone come along and suck 'em up with a vacuum?". This is a nod to another GameCube game, Luigi's Mansion.

By using a cheat device, you can access a test room. Certain beta elements are in it. For example, a soccer ball, along with a Hinokuri without its outer shell.

Each location on Isle Delfino contains an Italian word. This is likely in reference to Mario's nationality.
• Delfino Plaza - Dolphin Plaza
• Bianco Hills - White Hills
• Ricco Harbour - Rich Harbour
• Gelato Beach - Ice Cream Beach
• Pianta Village - Plant Village
• Noki Bay - Shell Bay
• Pinna Park - Fin Park
• Sirena Beach - Siren Beach
• Corona Mountain - Crown Mountain

The option to turn off closed captions during cutscenes does not appear in any non-western releases. This is likely due to cutscenes having extensive English voice acting in all versions of the game.

Within one of the bell towers in Delfino Plaza is a Rocket Nozzle box. The box is inaccessible without the use of a cheat device, and is only visible through the use of camera glitches.

The layout of the beach in the Sirena Beach stage strongly resembles the GameCube controller. One of the pools represents the grey analog stick, while the others are the A, B, X and Y buttons. The flame at the center is the START button, and the chairs are where the Nintendo GameCube logo would be. The two cabana huts are positioned to form the D-pad and C analog stick.