5th and 6th Ascendancy Points

In cruel difficulty after searching traitor's passage and killing boss for the relic to start the trial of Sekhamas I completed the trial and was not awarded ascendancy points or any interactable to do so. After leaving the quest told me to start over but the boss in traitors passage no longer drops the quest item that was used in the successful run I had earlier. After doing the quest and having no idea if I'm losing out on 2 ascendancy points or not is leaving me pretty frustrated.

I'm at the same point.
Apparently, third ascendency comes from maps in late game (monsters will drops sanctum item with 3 or 4 floors) and not from the cruel difficulty acts. The UI is bugged for this as it indeed tells you to search Traitor's passage, but you can ignore this.