The game contains unused data for an enemy named Iwagen that attacks by shooting rocks. It is a combination of Iwa, which is Japanese for rock, and gen, short for generator.

Normally, when starting up the game, a sound clip of a Pikmin saying "Pikmin!" accompanies the Nintendo logo. On rare occasions, though, a different sound effect will play. These include:
- "Whoo!", the sound effect of a Yellow Pikmin obtaining a bomb rock
- A Pikmin sighing
- A Japanese voice saying an unknown word

The Gamecube disc for Pikmin actually contains a Windows executable file. When run on a computer, the game will launch in a very glitchy state. In the game's debug menu is a mode titled "Game-Mode". Enabling this mode will fix several issues.

The two lights on the front of the ship change colors with the amount of progress Olimar has made in repairing it. The lights are off when he first crashes at the Impact Site. They are red when the Forest of Hope is accessible, yellow when The Forest Navel is accessible, green for The Distant Spring, blue for The Final Trial and purple when the Secret Safe is returned.

Olimar's ship, the S.S. Dolphin, likely refers to the code name of the Nintendo Gamecube: Project Dolphin.

If the memory card in slot 1 has a Pikmin save file on it when playing Super Smash Bros. Melee, the player will receive a "Captain Olimar" trophy.

Hidden in the the top-left area of the title screen is the name Toyoda written vertically. Tokihiko Toyoda was the designer in charge of the interface.

If down is pressed on the D-pad (Or 2 is pressed in the Wii version) Olimar will lay down and four Pikmin will carry him back to their Onion. When he is attempted to be taken inside, he will bounce off it and fireworks will shoot out the top of the onion similar to how Pikmin seeds are shot out of it.

Bulbie, Olimar's dog (Or at least a Hocotatian form of one), was the inspiration for the Bulborbs' names because of their resemblance to Bulbie. The Grub-dog family (Which includes Bulborbs among other creatures) was also named after him, due to Bulbie being a dog.

Pikmin was based on a tech-demo titled "Super Mario 128", and was designed to showcase the Gamecube's ability to utilize multiple AIs. The demo featured 128 Marios dismantling a pseudo-8 bit Mario sprite composed of several blocks by picking up and carrying them away. The demo also featured the ability to warp the terrain, which influenced the free-form gravity in Super Mario Galaxy. The demo later became Pikmin after Shigeru Miyamoto asked his team to create an entirely new game that would be nothing like a sequel to a Mario game.

Due to how high up the Libra ship part is, there is a chance that it could fall and bounce out of bounds with no way to get it. Since ship parts do not reset when the day ends, the Libra will be stuck there unless the player resets the game without saving. This also locks the player from getting the best or good endings that playthrough since the Libra is a mandatory ship part.

One of the ship pieces you can find in the game is a Geiger counter, though Olimar says he doesn't know what it is he notes that it goes off constantly, and the needle on it always seems to be moving. Since Geiger Counters are used to measure radiation it would imply that the seemingly humanless and vastly different earth of the Pikmin series was caused by Nuclear war.

Unused textures left in the game reveal that, at one time, it was intended for Pikmin types other than yellow to be able to carry bomb-rocks.

There's an unused Goomba model left on the games disc titled "kuribo.mob". Kuribo is Japanese for Goomba.