I'm having the same issues and I think the problem is PowerNap.
I'm not keeping a diary of the reboots but I think that the reboot happens when I put my MBPro retina on charge before going to sleep.
Since the lid is closed, the mac SHOULD be sleeping too, and not crashing, unless something is happening in its sleep... here it is, PowerNap, which on most Mac is active just when charging (look on System Preferences/Energy Saving/)!
When on PowerNap my sleeping Mac actually updates calendars, email, etc which is nice, but most of all "tries" to update the TimeMachine backup. What if finding a non TimeMachine drive, or not finding any disk at all (which is more likely) makes him angry?
I've just disabled Powernap, both on battery and when charging, and wait for it to happen again.
Any update to this? Did disabling powernap resolve your sleep/wake failures? I have a Gen 1 Retina MacBook pro (Mid 2012) and I've been getting constant sleep/wake failures for the last few months.