When I was going to use my Energy (specifically the Light and Dark Side battles energy) to farm two units, I don't remember losing energy from it. Although I did not have any bonus energy that was past the cap. (at least that's what I remember, and I trust my memory here) I went to double check the units and their battles were indeed farmed. I also remember before I farmed them I wouldn't of had enough Energy to farm both of their battles to the max without getting bonus energy from crystals or somewhere else, but I their battles were still maxed out anyway.
There's a chance it had to do with some weird internet things, like me only being able to use cellular data. The whole update was also not completely downloaded either. (It let me play as there was content that it would download as i entered it, like for example 133 MBs needed for me to enter the Store)
