My problem sounds like what is discussed in this thread, so I add my 2 cents to it:
My setup is a 2013 Macbook Air, hooked to a TBD (with several stuff hooked to the TBD like FireWire ElGato Sat tv receiver, USB hub with sticks or iPhones and one or more external USB hard drives) . Not always, but often when the MBA goes to sleep and I try to wake it by magic mouse click, the screen stays black.
This problem only appeared after update to 10.11 (or around the time when I did the update in November).
What helps for me is to unplug the TB cable from the MBA and replug it again. Then the screen comes up again. Doing so disconnects everything connected via the TBD, like FireWire EyeTV receiver (including interrupting potential running recording jobs) or USB volumes with open files. Therefore this is not a comfortable workaround in every situation.
What helps as well is to connect to the MBA via RemoteDesktop from another Mac. This shows me, that the MBA is awake and that it is only the TBD that does not wake up correctly. When connected via Remote Desktop, I see the screen of the MBA in the default resolution of the TBD. Navigating to the System Control Panel for the Monitor and changing the resolution to something different than the native one, makes the TBD show a picture again. Afterwards I can set the resolution back to the native TBD one and everything works again without interrupting the connections. Due to another Mac necessary for this procedure, it is not a comfortable workaround as well. That's why I hope that Apple will take care and present a solution for the issue with the next MacOSX update. 10.11.3 that would be.