First 2 Atlas points cannot be allocated into the tree

I guess this is an ongoing thing, I also read the book and got 2 Atlas skill points that flashing on my screen but I cannot allocate that to any Atlas points.

Usually this is because those points are for e.g. the boss tree at the top, or one of the other special trees around. Not the main Atlas tree.

I have this issue too and it is not because they have to go into a different tree... I also tried to pick up book with full inventory, then dropped something picked up and consumed book and it shows I have 2 points on screen but not showing in atlas...

I have a feeling those "unusable" points are for other trees. Check the number below each tree, it will tell you. If that's really not the case, I guess that's a bug when looting with full inventory.