I've been having this problem a lot and it's becoming extremely irritating.
So, I force quit an app (mostly Chrome, Steam and uTorrent) that isn't responding and open it again (this is also the situation when I force quit an app that is bouncing and won't open), it bounces for a long time again, so I force quit again, it keeps bouncing for a while and then 'quits'.
But, you can't open it, and when you right click it, it has the same options it would have if it were open. It appears in the force quit menu, but won't quit. It doesn't appear in activity monitor anywhere. Now, I know an obvious solution is to hardware shutdown, but my macbook pro is under a monitor stand and I would have to move a lot of hardware every time it happens.