The boss Phoenix Magnion has an attack that summons ghostly images of the characters Vile, Agile, Bit and Colonel (who were introduced in Mega Man X1 - X4, respectively) to attack Zero. Interesting facts to note is that two of the enemies, Agile and Bit, are never actually met in gameplay by Zero in either X2 or X3, and Bit, for the first time, is seen in gameplay using his shield that was formerly only seen in concept and other official art, not gameplay.

Despite dying in Mega Man Zero and not appearing in Mega Man Zero 2, Phantom had an Armed Phenomenon form concept similar to the forms added for the other three remaining X Guardians.

During the cutscene in the Temple of Wind, when Elpizo dashes away after triggering Harpuia's Armed Phenomenon form, a 1 appears behind his foot and a 2 appears under his head. This was removed in the Mega Man Zero Collection.