So the "corpses" I was supposed to be getting turn into materials?
I meant the corpses of the dead, not just materials from them.
The materials *are* the corpses. In battle, all of the corpses you see are an item defined on their respective armor rulesets called 'corpseItem.' When you end a battle, all of the corpses that are recovered check their respective armor ruleset definitions for a line item called 'corpseGeo,' and are recovered as whatever that item is. For mutants in most armors (including your gals), this item is Rare Earth Elements. For low-level Guild, the item is Durathread Mesh, and so on. In order to get both a corpse (say G.O. corpse) and a material item (the Durathread Mesh), you'd need to add for each corpse item a manufacturing project to produce both. In other words, from that dead G.O. in the battlescape, you'd get the item Dead G.O., which you can spend a few runt-hours to get one G.O. Corpse and one Durathread Mesh. This is rather tedious and generally a waste of the player's time for little benefit, as the corpse would only be good for selling and just a measly amount at that when you could have had your runts keep producing Grog.
On the other hand, Deep Ones and many other animal-like enemies get an extraction manufacturing option from their corpse, giving something that can be turned for a profit (cooking the tasty Deep One meat), or something to be turned into a useful item (Chitin Plates from Lobsterman => scale mail armor), after certain research is done. This isn't a waste of the player's time, because it is a less common enemy that turns a better profit than just Grog, but you have to make sure you have the storage space for all these corpses.