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.

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.

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.

The Nintendo Switch port of Pikmin 2 redesigns the game's treasures to replace all instances of real-world product placement, most likely due to licensing issues. In its place are generic versions of the same or similar goods, with the exact method of alteration varying from treasure to treasure.

Some replace the real-world brands with fictional ones, such as Duracell batteries being rebranded "Super Battery," Skippy peanut butter becoming "Ribbon's," and Tree Top apple juice becoming "Fresh." Others are replaced with unbranded counterparts; some cases, like Kiwi Shoe Polish, Chapstick lip balm, and French's mustard simply scrub the brand names, while others change the product entirely, such as Underwood deviled ham becoming tuna salad, Carmex cold sore ointment becoming hand cream, and Vlasic pickles becoming orange jam. Curiously, the Durable Energy Cell's name goes unchanged despite being a play on the now-excised Duracell brand.