This kept happening when my friend and I decided to try farming him for a bit before moving onto something else. Sometimes I'd aim right over his dust cloud and nothing... And sometimes when we kept "missing," he eventually popped out of the ground anyways. o.o Was so weird and glitch-y.
Edit: Also, you can get at least as much as three essences from beating him. I got between 2-3 per fight, while my friend only got 1 each time(she is lower level than me).