Too Many Atlas Passive Points?

After completing the Sealed Vault map I received 3 Atlas Skill Books. I believe they were Atlas Books 1, 2, and 5 all after finishing the Sealed Vault map. I had done this map earlier in my atlas, so I don't think I should have received any skill books.

Anyway, being curious I click each one to receive +2 skill points each for a total of +6. Before this point I had 38/40 Atlas points, now the game is attempting to say I have +6 more points, which would be 44/40. I can't allocate any of these +6 points, and therefore it is now stuck on my screen.

I don't know how to add an image on this website, but I would appreciate any way to remove the notification if possible.

Are you sure the points aren't for other sections of the Atlas tree?