If the player manages to scan the projectiles that the Omega Pirate fires, the description will consist of placeholder text that reads "This is an Elite Space Pirate" on the first page and "Elite Space Pirate description 3" on the second. Not only does the later Japanese release retain this oversight, but it also introduces a second one, in that the placeholder text is still in English.

The North American physical release of Metroid Prime: Remastered has reversible cover art. In the same way that the North American release's cover art was remade, the reversible cover art features a remake of the artwork used for the Japanese release of the original game. It's currently unknown if the Japanese physical release will feature reversible artwork from the North American release.

An unused version of the Phazon Suit can still be found in the games files, which takes a more blue/turquoise color scheme as opposed to the final black-and-red version.
Senior Artist Mike Sneath commented on it, saying "Yes you are right that is what was another version of the Phazon Suit which was done by another artist Gene Kohler. Gene made all the suits with the only exception being the black phazon suit. That suit you mentioned was cut because if I remember the Art Lead Todd Keller didn't feel the suit felt evil enough. That was the whole idea about liquid Phazon is that it transforms things into being aggressive and destructive and Todd wanted that to be reflected in how the suit look. That is all I can remember with regards to that suit you mentioned and I hope I got the story right on that as it was a long time ago but I believe that is why it got cut." [sic]

A fully-textured model of a Ripper from earlier Metroid games can be found among the Phazon Mines files. The hook on the bottom suggests that they may have been used as grapple points. They were probably replaced with Gliders, which serve the same purpose, and are found in the Phazon Mines as well as in Phendrana Drifts.

Originally, Samus was going to give an opening monologue establishing the back story for the game. Though the narration was cut in the final product, a clip with Jennifer Hale (Samus's voice actor) giving this narration can still be found on the game's disc. This was also the inspiration for the narration in the "Opening / Menu (Metroid Prime)" music for Super Smash Bros. Brawl.

The hand symbols on the icons for each beam type in Metroid Prime evidently represent the gesture Samus must make with her hand in order to switch between beam types. This can be seen by switching beams while using the X-ray visor.

Using the GameCube"“Game Boy Advance Link cable to connect a completed game of Metroid Fusion to Metroid Prime unlocks the original NES Metroid game and Samus' Fusion Suit for use on Metroid Prime. Both games must be completed before the Fusion Suit can be worn, but it has no special features, and is purely aesthetic.

There is an unused scan image of what looks like a Shinesparking Samus. In an interview with Retro Studios, it was revealed that they were considering implementing the Speed Booster and Shinespark, but due to the difficulties implementing it, it was scrapped.

Kraid was intended to return as a boss, but was scrapped due to time constraints. Kraid's character model was completely finished, but the there wasn't enough time left to create a fully polished boss fight.

"It was decided that Kraid was not imperative enough to the Metroid Prime project to run the risk of pushing up the release date in order to fit him in." -Gene Kohler

During development, a flying insect-like enemy was removed from the game. It is speculated that it may have been an early design for the aerial pirates or possibly intended to serve as a boss at some point in the game.

During development, a four-armed gorilla enemy, possibly intended as a boss of the ice area, was removed from the game. Nintendo felt that some of the early models looked too much like monsters designed for an RPG and decided they did not fit in the Metroid world.