While doing some Explorer's Case: Skyhold i noticed always getting the same ressource from one node. Upon inspecting the log i only saw 5 inventory notifications regarding received ressources per chart.
So one node always showed the same ressource in the interaction, the interaction completed the step for that node, but no ressources are received in inventory.
Changing to another instance fixed the problem.
The node in question was the one closest to entrance in Skyhold and always showed the new ressource: Ebony Log.
Maybe adding the new ressource also added a bug.