This is a common problem with a few of the quests. I'm not sure I know the specific quest you're talking about but the items will have to be picked up manually. ie you're character will have to locate them on the map, you'll have to hold down ctrl key to change the cursor to a grabby hand, and pick it up.
Holding down ctrl will highlight items available to be picked up making it easier to find the item.
The major issue here though is this, often these items whilst they show up on the inventory list have left the map. Explosions, usually from grenades, can cause items to leave the physical map. If you can't find the items needed on the map, probably where the bulk of the enemy first spawned, then you'll need to reload and play out the whole fight again noting where the items are early in the battle and avoid using grenades in that vacinity.
Good luck.
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