VGFacts

It is possible that the Ing possessing the body is the one that stole Samus' original Missile Launcher at the beginning of the story, given that the Missile Expansion it drops looks like the Missile Launcher as opposed to a regular Missile Expansion. However, it is logical to think that the soldier, prior to its death, had the Launcher item equipped to enable it to fire its missiles (similar to how Samus requires the Morph Ball to drop Bombs). Also, the scan of this darkling suggests it indeed had the weapon prior to Ing-possession.

http://metroid.wikia.com/wiki/Dark_Missile_Trooper

this may be a beta element for metroid prime 2: echoes. Perhaps you were origonaly going to face the dark missile trooper for the missile upgrade, and not find it how you do in the game now.