Version 2.1.8
If you import assets from FBX files you often do not have that much freedom to define where your RigidBody3D node is in the scene tree. So, you can not ensure that the RigidBody3D node is the top node for picking (and removal). For this case I added a variable to define these comfortably in inventory-system-demos/character/dropped_item_3d.gd:

Set the "Remove Node" property to the top node and you are done.
We also have to adapt the inventory-system-demos/character/character_inventory_system.gd to handle this correctly:
