I posted the text below almost as-is for the 3.14 release, only later finding out that no, this bug is still present. So here goes again....
It's mainly on the file manager (that I've found) but you can click OUTSIDE the window and still interact with the window. For example if you have two file-managers close to each other with another window below them both and visible in the gap then you can't click the lower window directly even though you can see it and put your mouse over the visible part of it. All you do is focus one or the other of the file manager windows.
You can also hold down the windows key and click outside the file manager window and drag it around the screen just as if you had clicked inside the window (I can't remember if I changed the default key from alt to windows in my settings but the point applies).
Generally I'm OK with Gnome3 (providing you get the right extensions) but these invisible borders are such a fundamental breakage of the basic concept of a graphical windowed user interface.