The song that plays during the game's final boss, Spoiler:the Titan Dweevil, has 11 alternating sections and musical cues, more than any other boss in the Pikmin series. The conditions that trigger each theme are based off Spoiler:the treasures it wields, from the number of treasures present to the particular one in use. The boss also has its own unique attack preparation cue, defense cue, and "defeated" cue.

In 2019, a second instance of Totaka's Song appearing in Pikmin 2 was discovered 15 years after the game's original release. By entering any cave without a Memory Card inserted into the Nintendo GameCube, the "Pikmin 2 Memory Card Check" screen will appear advising the player to insert a Memory Card so the game can save its data, and will play quiet ambient music in the background. By waiting on this screen for roughly 3 minutes and 40 seconds, Totaka's Song will play.

In the Japanese release of the game, the silencer item is worth 666 pokos. In all other releases, it is worth 670 pokos. Since the number 666 is associated with Satan in Christianity, it was likely changed to remove this connection in the West.

Pikmin 2's soundtrack contains many variations of the same songs, switching between variations based on what is currently happening, such as Pikmin carrying an item, enemies being nearby, or if sundown is occurring. Most of these variations add or remove instrumentation compared to the normal track, but if the player is controlling Louie or Spoiler:The President, the beat of the music is also given additional syncopation.

By looking at the Implement of Toil treasure, the brand name is "Nintendo 64", after the console of the same name.

The Decorative Goo and Master's Instrument treasures have the brand name of "Mario Paints", a reference to Mario Paint on the SNES.

Pressing certain buttons on the title screen leads to a number of easter eggs, including spawning a Red Bulborb or Iridescent Flint Beetle, manually controlling the spawned enemies, and rearranging the Pikmin to spell out "Nintendo".

The logo on the Flame of Tomorrow treasure features Bowser, from the Super Mario franchise, but only in the US and European versions. In the Japanese version, the brand is instead listed as "Sun Breath", and the Bowser illustration is removed.

The Cosmic Archive treasure is a Famicom Disk System disk card for Nazo no Murasame-jo (later localized as "The Mysterious Murasame Castle").

In the games files, there are unused placeholder graphics from the game Mappy. Interestingly, the game was made by Namco Bandai, who also worked with Nintendo on other games, including Star Fox: Assault, and Mario Kart Arcade GP.

Many of the game's treasures were changed when the game was localized in different regions. Many of the treasures in the original Japanese game were based on Japan-only brands and cultural references. These were changed to more appropriate brands and references in each region. This is the reason why Disk Mystery-based treasures are Japan-only, as well as the Survival Series being US-only.

Unused Data in the game includes a 7th Pikmin type (the 6th being Bulbmin). Hacking the game and giving the player this type reveals they are actually Pik-Pik Carrots. They don't have much animation, and they float a bit above ground. Their stems always have a leaf on top, even if a bud, flower or spicy glow overlaps it. It also glows green when idle, like Bulbmin. They act, react and sound like any other non-Bulbmin Pikmin, and have no special attributes or defences. Finally, on the HUD, their "standby Pikmin" icon doesn't exist, and they get skipped over when calculating the closest Pikmin.

Graphics for a game over screen exists in the game's data. Most of the graphics are the same as in other screens, but two of the textures are the words "GAME OVER" (one of them is likely an alpha channel). This texture is present in all versions of the game, and in all regional folders in the data.

GameCube discs of Luigi's Mansion, Super Mario Sunshine, The Legend of Zelda: The Wind Waker & the first Pikmin game were originally going to appear in Pikmin 2 as unique treasures to collect. Their textures can still be found in the game's files. This idea would later be revisited in a pared-down form in Pikmin 4, in which the game disc for Wave Race: Blue Storm is obtainable as the Glinty Circular Disc.

About 30% of the game's floor layout files are unused.

There is early English script for "Louie's Notes" that usually can't be viewed outside of hacking/cheating. All of Louie's Notes were changed during development. There are also 6 missing entries, suggesting they didn't exist early in development. They are:
Spoiler: "Hairy Bulborb"
"Decorated Cannon Beetle"
"Volatile Dweevil"
"Toady Bloyster"
"Segmented Crawbster"
and finally, the Spoiler: "Waterwraith".

Several pieces of information in the game hint that Louie was actually controlling the game's final boss, the Spoiler:Titan Dweevil.

Because Olimar is carrying a bottle cap in the game's intro, it would mean he has the strength of at least four Pikmin.

The game's files list the captain's folders as "orima" (Olimar), "orima3" (Louie), and "syatyou" (The President). The captain "orima2" was removed and was speculated to be Olimar's son.

By going to any dungeon you have not completed and getting every treasure there, you will be brought to a special results screen. By waiting at this screen for about four minutes, Totaka's Song will start playing.