Here is my launcher when I open Nautilus with its corresponding icon (top one). It's supposed to stay on the top icon, not create a bottom icon.
I wonder what causes this behavior, because it really annoys me. I have tried replacing the original icon with the new one, but I've realized they're different, so I won't do it (there's a new "Open a New Window" option, that's the difference).
I have had this problem since I upgraded to 16.04 yesterday.