During development, a strange looking enemy that shares a similar model with two enemies from previous games was removed.

Metroid Prime Hunters is the first and so far only Metroid game to not have Metroids in it.

It appears that the models and textures for each of the characters were originally far more detailed than the downscaled assets in the final game.

Concept art reveals that space battles against other bounty hunters were once considered by the developers at an early stage of the game's development.

Despite this game not featuring Metroids, in the demo version (Metroid Prime Hunters: First Hunt) the primary enemy is the Mochtroid. Mochtroids are failed Metroid clones which previously had only appeared in Super Metroid. They are distinguishable from Metroids as they have fewer nuclei, are far easier to kill, have an all around more sickly look (they are not as spherical or well developed as a true Metroid) and have trouble latching onto their victims (you can walk out of them, whereas to unlatch a Metroid you must use a bomb).

Hidden in the yellow flash of light that separates the game's introductory credit sequence and the character introduction videos is Spoiler:Gorea, the primary antagonist of the game.