Cannot spend atlas points earned from books

I died and couldn't return to the map. The map included my first encounter with
Dannig via expedition and my first boss. Map was Tier 1

Dannig and Zelina awarded me atlas point books, totaling 4 points. I am unable to allocate these points. Later on, Alva, awarded me a book after my first delirium map (this map was completed successfully). Again, cannot allocate the points.

I have 6 points that I now cannot spend. I'm unsure if my altas needs to be reset, and my searches have turned up no similar situations. I have verified files, and reinstalled the game. It has not fixed it.

Update: it is now 8 points since finishing my first breach. I am able to allocate points granted by defeated corrupted nexus, just not the books.

Having same issue, recived Dannig quest skill book and cant spend those points

Yeah, this is a bug.
I am getting the same issue as well.