In Ubuntu 16.04: when I run
sudo nautilus from the terminal, a new window pops up but no arrow indicating an opened window appears besides the nautilus icon at the unity panel. When I minimize the root window and then click again on the icon, instead of opening the root window, a new non-root window pops up and suddenly two arrows appear near the nautilus icon. (Not even scrolling on top of the icon works to show the minimized window.) When I close the non-root window, only then the arrow indicating the root window stays on the panel and everything works like it should.
I also tried removing the nautilus icon from the panel and run
sudo nautilus from the terminal. In that case a new icon appears with the arrow and everything behaves normal.
Is there a way to fix this? It is annoying.