macOS Sierra lost focus Finder when using mission controls
I'm having exact the same issue, and it took me weeks to define it, while it was driving me crazy. Its clearly a bug, and the update 10.12.1 didn't work. But, there might be another solution. I've followed your advice and assigned finder and safari to different desktops, it works but its not the way it should be. However, assigning finder and safari to NONE works!!! I've tried to juggle with a few different apps and so far so good