I've run into an annoying issue with Sierra. I typically run four or five desktops in Mission Control (and have since Lion) to group tasks on their own screen space. This is on a late 2012 mini, which I installed a pair of SSDs into and then did a network-install and then upgrade to Sierra before loading any apps.
If I have a window in focus and pull up Mission Control, and select Dashboard, it switches to the dashboard, but then almost instantly switches back to the active window I was just in. I have to minimize the active window to get the switch to stick. This is not limited to just trying to use Dashboard, which I admit I almost never do, usually I'm trying to switch to a different desktop space to go looking for a file in Finder for a reference. This leads me to another annoyance that is related.
Prior to Sierra, if I had minimized an application, and later used CMD-TAB to switch back to it, it would pull it back up to the desktop space it was minimized from, show the application and switch to it. Now, it accepts the selection, but does not restore the window. It does bring it up on the ribbon, but I usually end up going to the dock to restore the application to where I can see it.
Question is this, where are the settings for these behaviors? Hopefully its a trick setting somewhere I can toy with, but so far I've not found anything that seems to tame these issues. I'm about ready to nuke the drive from orbit and roll back to El Cap or Yosemite, as these two issues are fouling up several years of work flow habits.
I've seen several posts like this one on Finder loosing focus or this one about strange Mission Control behavior with the Dock that seem in the same neighborhood as my issues. For that matter this one about auto-swoosh is close too.
I've had my issue strike with Firefox, PHPStorm, Atom (GitHub's text editor) and the GitHub app too, TextWrangler, iTunes (12.5.5.5), Facetime, Messaging, and Launchpad. I wonder if its not a fouled system hook for the little magic bar thingie on the new MacBookPro.
Best Answer
This sounds like it is a MacOS issue. My 1st recommendation would normally be to update MacOS but I would recommend that you backup your Mac and then reinstall MacOS.