Twice now I have been in MP in a Nexus mission that required gathering. Both times, when I reached the depot for the dropoff, the gathered items were not in my pocket.
Update: I opened my file in save editor and my hadal cores were there…but they do not show in-game
Some games protect “quest items” from being sold accidentally by hiding them or displaying them in a different category – but hiding them from the poor quest recipient is a bit much, HG, give them back! 
I haven’t tried a real QS mission recently (I only did the expeditions) – did this happen only once? Sometimes there are several variations of a mission and one has a wrong text/variable, so every x times it looks broken. Maybe this is another broken variant?
It has happened twice now. 2 different gathering missions for different items. When I get to the depot to hand them in, the words are grayed out and they do not show in my suit pockets. But they do show in my pockets in save editor.
Reporting it.
Another observation on quests in MP. For the last few days my friend has been successfully doing mission agent missions in single player. Last night we fired up MP and various of his missions failed. One was a gathering mission and when he went to turn in the object it took it, reported success, did not advance the mission and proceeded to tell him to turn it in (again, multiple times). He vacated that mission started another to scan minerals, every scan told him he collected 1/-1 . It was late so we didn’t explore this any further, maybe tonight.