This problem has been around for at least a year on multiple Sierra versions.
When I’m switching to another app through Mission Control it focuses on that app only for a split of a second and then switches focus to another app. Here’s the video showing the issue (it switches back to Evernote.app despite clicking on the Finder.app):
It seems that the app that is set to be visible on All Desktops loses focus if you are switching from an app that has been set to some Desktop (Desktop on Display 1, 2, etc.).
What is the solution to this problem?