Atlas tree skill points bug

I was clearing the atlas map to get more atlas skill points. After clearing corrupted nexus i didn't get skill points. I thought i used lesser lvl waystone (i neeeded lvl 4). After i found another nexus i checked i use right waystone and cleared it. And still nothing, Doryani just don't come to give me atlas tree skill points. Am i doing smt wrong . How do i get my skill points from cleared nexus?

I had a "knowledge book I" that said it would award 5 Atlas Passive Skill Points but I only got 2. Is this a bug or am I missing something. I have a Crystalline Core of Knowledge II and I am afraid to right click it in fear I won't get 5 atlas passives.