After completing an Extreme (private) Swamp Vault, I was surprised when there were only 2 essence bundles after defeating the boss -- the one at the base of the ramp, and then one more next to the exit portal. My Desert Vault runs routinely had 5 or so essence bundles after the boss, and asking around on the Discord indicates that this is the intended reward, so there's possibly something causing end-of-vault Essences to not spawn in properly.
Happened to me once when I soloed the desert vault at the Watch and died over 50 times trying to kill the Sun Giant. I only got 2 essence bundles that time. I thought maybe I was punished for taking so long to finish or something.