Anyhow, this is typical when an app has hung. Usually you have to force quit that app.
I have two monitors and I run into this issue quite often. Where for some reason the application window in mac remains hidden. For eg. I can go to the menu of an application say 'Firefox' and select the 'Window -> <Title of tab>' but the Firefox browser will not appear on any of my two monitor, the menu will remain active. There is no way to get to the window. Even via mission control. If i right-click on the Firefox browser in the dock and hit 'Show All Windows' it will show the open window in a border. Clicking on it will not bring it to the front but the remaining application will come back.