Seven Force, a boss from Gunstar Heroes that appears in this game as the boss of the Underground Mine stage, was originally intended to have two extra forms: Harpy Force and Nemesis Force. These forms were never finished due to time constraints, but voice clips of the game's announcer saying each form's name can be found in the Voice Test, and their idle sprites can be found in the game's data.

An unused boss resembling a hand can be found in the game's data and can be fought in Stage 13 through hacking. This boss was featured in pre-release screenshots of the game, and was named "Love Penguin".

An unfinished boss resembling a cowboy rabbit can be found in the game's data. This boss has an unused animation depicting it firing its gun. According to an early sketch of the game's cover art by Hideyuki Suganami, this boss was named "Lambda Bunny".

Sprites for an unfinished dragon boss can be found in the game's data. This boss has no working code and cannot be activated in-game.

Treasure president Masato Maegawa and Alien Soldier director Hideyuki Suganami had big ideas in mind for the potential of the game's bosses, with two ideas being thrown around to add a boss with 100 or even 1000 transformations, or a boss with 100 moving/multi-jointed parts. Neither of these ideas were added due to time constraints, but Maegawa still took pride in this early idea for motivating them to further develop the multi-jointed sprite animations in the final game.

Alien Soldier’s credits tell the player the total amount of damage they took throughout an entire playthrough. Originally, some kind of reward was going to be given for beating the game without taking any damage, but the development team ran out of time before this could be implemented.