Last 4 days, I encountered this problem twice. I'm using my Retina Macbook Pro 13" (OS X : El-Capitan) with a Thunderbolt Display (+ third party mouse and keyboard plugged into the TBD) since about two weeks now.
I tried waking it up by opening the lid, no display (absolutely, not even a black screen), unresponsive keyboard, I tried turning it on using the power button, I had to press it (and hold it) many times before it responded (finally), showing a message in multiple languages in the likes of
Your computer was shut down because of a problem, and when I logged on this dialog box appeared:
("shut down" instead of "restarted", this picture was found on web)
Everything works just fine after the occurence of this SCARY problem.
I use two (famous) software that that require disabled SIP: SwitchResX and Karabiner.
syslog | grep shutdown had to say about the issue :
Sep 29 17:54:40 localhost kernel <Notice>: Previous shutdown cause: 3 Sep 29 17:54:40 localhost locationd <Error>: locationd was started after an unclean shutdown