Mid '11 Mac Mini won't shutdown cleanly. OS X El Capitan 10.11.6 When I go to shutdown my mid 2011 Mac Mini (running OS X El Cap, EDIT* 10.11.6), it will not do so "cleanly." I close all applications, then click Apple > Shutdown and finder closes like it's going to shutdown, but it gets stuck. I have to hold the power button till it shuts down, then when it powers back on I get the error message (with a yellow exclamation point): 


  You shut down your computer because of a problem. If you want to open the applications that were open when you shut down, click Open. If you do nothing, the computer will continue to login in 17 seconds...


So far I have tried:
 - Opening Disk Utility and running "First Aid" on the SSD. I get a green check mark when done.
 - Booting to Recovery (Cmd + R) and running First Aid. 

EDIT: Apparently "First Aid" is not the same as repairing disk permissions! Looking into this... http://osxdaily.com/2015/11/04/verify-repair-permissions-mac-os-x/  

EDIT2: As a result of the issue, I am unable to install any OS X updates and the only way I can reboot is via the terminal command sudo reboot now 

EDIT3: Booting in verbose mode, I see many (about 20 or so) of these:
Could not open PlatformSupport.plist
and also...
ERROR!!! Recovery Image verification fail with status [0x800000000000000e]
Error loading kernel cache 0oxe)

What could be the issue here? Anyone know what logs files I can check and where? Thanks.
Firstly, you should update to OS X 10.11.6. It will solve many problems. Download 10.11.6 Update.

Secondly, reset SMC. Here is a link how to do it: Resetting System Management Controller.

If it doesn't help, try clean install: How to Clean Install El Capitan.

ADDITION:

If you can't do clean install using your own mac, make a bootable USB on another mac: Click here.

Also, go to Utilities and run Console.app for inspecting what's wrong with your OS: Click here.

It might be a problem with a hardware, so try single-user mode pressing cmd-s after startup 'chime' sound or verbose mode pressing cmd-v the same way. To read about it Click here. 

And read an important post about 7 Mac Startup Options: Click here.