Stuck inside the vaal room/Atlas passives skills points

I'm inside the Vaal Temple, the doors to the room are locked, there are no more mobs to kill, and I can't open a portal or leave.

I'm also earning Atlas Passive Points from the books, but I can't add them. I've already used two books, the icon appears showing that I earned the 4 points, but when I open the Atlas Three screen, it counts as 0/40 and I can't add the points.