Okay, so I have been fighting in battles, and I always lose energy, in manual or auto, yet when I fight and win i manual, I lose energy, but the auto pet doesn't. But when my auto pet loses a fight it loses energy.

Can someone please explain this to me?

You're fighting against a gladiator pet. The gryphon Gladiator gene prevents energy loss whenever they lose. So its nothing to do with whether its manual or auto fighting - A gladiator gryphon can lose infinite times and still keep on going. 

Just like the Energizer Bunny. :P