The option to turn off closed captions during cutscenes does not appear in the Japanese release, likely due to them having extensive English voice acting in all versions of the game.

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

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.

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.

Within the game's data is a sound file of Mario saying "Ciao"; this is meant to have a 1/8 chance of replacing the coin sound effect that accompanies the Nintendo logo when booting up the game. However, due to a programming error, the random number generator for this sequence is initialized at 0, resulting in it never rolling. Consequently, the "Ciao" voice clip cannot be heard in the normal course of play.

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.

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".

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!"

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 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, 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.

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.

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.

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.

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.

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.

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 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 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.

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.