The Silent Cave map completion bug (no atlas skill points and map fail)

Just did this map for the first time. I killed all trapped enemies first to power up the boss, used a vaal orb on the boss to try and change the rewarded essences, killed the boss, loots drop but no atlas skill point book that the game told me I would get. Left the map and now map said it is failed even though I cleared everything in it. Pictures attached.

https://imgur.com/a/XkGzefP