So now, at the end of another mission I came into this situation:
One clip in my Inventory, one on the ground.
Resulting in this debriefing screen:
and this store screen, after return of my Chinook:
Last session I played in 16.5, I can remember picking up an alien clip, which showed up in my store afterwards.
Mods can feel free to move this thread into a proper sub-forum, or merge it with existing threads, should this be bug-section relevant.