I'm on Ubuntu 16.04.1 at the moment, and system windows like the Files window, Terminal or System Software open behind the Unity launcher, which means they are partially hidden behind it. I can move them with Alt+F7, but I'd like a more permanent solution to this problem.
Open CompizConfig Settings Manager and enable "Place Windows" under "Window Management". This should solve the problem.
A permanent solution that I personally use is to set the Unity Launcher to autohide. If you go into Settings ---> Appearance and then go into the "Behavior" tab, you can select autohide. I find the top left corner option to be optimal for unhiding the Unity Launcher. This way, the Unity Launcher will only be present when you need it. You can also reveal the Unity Launcher by pressing the "Windows" key.
I hope this helps!