I've been having this issue for a while now. I cant remember if it was a problem when I was using Mavericks, but I've only noticed it using Sierra.
Every time I initiate mission control (using either F3 or Three finger gesture upwards), if I click on a window, or even just want to return to the original window I was on, another open window comes to the front.
This issue is extremely frustrating, as I almost always end up having to click on the window I was originally on when I see it behind the other window that comes up.
I am using a Macbook Pro Early 2015 on MacOS Sierra Version 10.12.1