There could potentially be an issue or it could be the way item dropping is handled. When an item drops there's a chance that it will fall somewhere that is not immediately visible, and it will be placed in one of the post mission loot containers. Depending on the number of items that this happens to, either the first, or first and second loot containers will contain these items. If you saw an item being used and have unlocked both of the first 2 containers, and haven't gotten it, there's a problem.