Arduino Leonardo runs unusually hot
My Leonardo, which I leave on all the time, is not hot. The CPU chip feels at room temperature as far as I can tell. If you were powering something from it, maybe you are drawing too much current. If it gets hot just sitting there doing nothing, and with nothing connected, something is wrong.

Maybe you damaged it in the past? Maybe hooked up some LEDs without current-limiting resistors? If not, it sounds like a faulty device to me.