Since I upgraded to Yosemite, I've had the same consistent issue with Safari. I'll go to scroll and may accidentally scroll with multiple fingers, and the window gets stuck in the top of the page, leaving a somewhat transparent greay outline around my desktop. The window is stuck and won't move, and Mission Control becomes unuseable. It's the strangest thing and I have yet to find a fix for it and have tried all the general steps. Here's a picture for reference, though usually the window is stuck with the top half being unreachable:
