Thanks, Penumbra!
I discovered the source of my confusion: It seems that spell resources you pick up from the ground (as opposed to mission given ones) are not immediately also given to other players. Playing with my son, I collected many dozens of citrine wile exploring some caves, while he deforested a region or two and got hundred of plums and cherries. Then I checked his supplies, and he did not have any of the citrine I collected, and I didn't have any the cherries and plums he collected.
He exited out of the game and then I reconnected to check something, and saw that suddenly he had all the eextra citrine he should. So then I checked my character (which hadn't ewxited the game), and I was still missing the plums and cherries he had collected. So I exited my character, reconnected and all the extra plums and cherries were now available for me.
Is this expected/normal behavior, or should I put it in Mantis?