Keep an eye on it. If it does not happen again just mark it up to a fluke.
Things that it might have been:
If the smart cover was in a position to slide around a bit, it might turn the iPad on and off all night.
Did you have a bluetooth keyboard paired and on. Might do something.
If you started a large app download or other syncing process it could have continued part of the night, using up battery.
Also, I'm not entirely convinced that an active (open) app will always shut down when the cover is closed. It may simply turn off the screen and keep running the app. I once thought I saw unusual battery drain on my iPad when I left Safari open to a webpage that automatically updated it's content; with the cover closed. I meant to test that more objectively, but because it would take a lot of time and planning I never have.
To play it safe, always close the open app when you are finished with it. A few do have legitimate background tasks that can eat up battery.