The other instance I've come across is the Attunement Sphere that is also acquired as part of the main quest. As this item is weightless, it's less annoying, but having unnecessary items filling up the inventory with no means of removing them is frustrating.
Hopefully this issue will be resolved in the coming update.
A suggestion while I'm at it: If items flagged as quest items is a necessity, at least allow for the ability to store them in something owned by the player, namely a house chest or something of the like.
