No Spirit Gained from killing Bosses

I have completed campaign on both difficulties making sure to do all side bosses, quests, and full map clears. only one boss will not clear from my map and that is Rootdredge cruel act 3. Ive killed him 5 times. still wont clear. REGARDLESS i have a maximum of 60 spirit. were i should have more around 200. anyone have this issue where you are not gaining the proper spirit? this holds me back greatly in the end game...