MacBook Retina strange system/battery behaviour
macbooks generally hibernate (save your ram's state to your hdd) when the battery is too low.
to do that efficiently (without losing data) there's an internal threshold that keeps some energy for the system to save state.

in general, you don't shut down (as in "windows is shutting down") your mac. you either let it go to sleep after some time or just close the lid (and trigger hibernation). you can even trigger hibernation from the apple menu.