Atlas Passive skills Falsely rewarded

Currently I have 2 passive skill point notifications that i cannot spend.

I was in verdant wildwood waystone, i died, upon re-entering i was able to pick up a book of knowledge 1 book and use it to get 2 atlas passive skill points. I then was locked out of instance and the darknesss would not let me progress or finish the map. i returned to hideout and zelina had a quest and rewarded me with another book of knowledge 1 book which i used. now i have 2 points i cant spend. i dont mind not getting double points but i want the notification to go away

please help

Check the other atlas trees. Points are not universal.