The Cleaner Mission, some soldiers picked up smgs and the ammo from dead cleaners while collecting data sticks. Mission successful, everyone returned to the ship, but when I arrived back at base, everything I had picked up had vanished. I checked the soldiers inventory, available weapons and the stores, but no smg's nor ammo... I have not yet researched how to make smg's, but I did expect that whatever I collect from the battlefield remains with my soldiers.
I'm not using any mods.