Not sure if this is just me, or maybe something to do with skill levels but would be interested if someone else could check this out...
I have the Refining I skill and I just crushed a batch of Sparkly & the energy usage wasn't reported consistently. If I crush 10 units, the activity window says it's taken 40 energy, my energy level goes down by 40 but the little popup that appears underneath the energy meter read "-36".
This scales similarly for higher/lower quantities.
Could someone try this & see what happens for them? Also try with different rocks & maybe Refining II.