The following happened to me twice in the dungeon for Barbarian (Legendary power that gives up to 10% damage based on primary resourse).
I ender the second level and fight an elite (usually a spider) before the pop up message for collecting Essence shows up. As a result, killing the Elite does not give me any essence.
In the end of the second level, there is not enough Essence to enter the boss room so I have to restart from the beginning (I scoured the entire second level a few times and every mod was dead so there was not way to get any more essence…).
My current fix is to first prompt the pop up message and later kill any Elites (even if they show up before the message).