Missing the +40 spirit and two weapon skill points

In both instance I lost them the exact same way, my inventory was full and after killing the boss I picked up the quests items (Shark Fin and Spirit Skull) it dissapeared from the ground but did not appear in my inventory or stash.

Reseting the zone and killing them again also did not help.

Any help would be appriciated!

Edit: Happened on my Titan in 0.4.0c

Do you have the Colossal Capacity and the quest items are in the extended inventory?