In gnome-shell when I try to close a window ,as soon as I hit the close button all mouse clicks are ignored , by that I mean that the mouse pointer moves but nothing , not the desktop , not the window I was trying to close , not the menu bar respond to mouse clicks , the keyboard is active so I can ctrl>alt>F1 and reboot from there . Interestingly running top from the terminal does not show the application I was trying to close . Prior to hitting the close button everything is normal .

Edit: this only happens in gnome-shell , unity and gnome classic (no effects) are ok .