App crashes, dock icon remains, can't reboot, yet no process in ps aux to kill

I've been encountering an extremely annoying problem since I upgraded to Yosemite. FCPX (but I've been having reports of this problem on other computers with finder.app and safari.app) sometimes will crash on exit (with no detectable log trace) and its icon will remain in the dock with the usual "this application is not responding" menu warning. Force quit won't work Rebooting can only be done the hard way because the stuck app is preventing a soft one yet no single process regarding FCPX is listed when in the activity monitor nor there is one in psaux. No zombie processes to be found; computer performance is fine. If I open an FCPX library, I'll get a dialog stating that "The application "Final Cut Pro" is not open anymore", which is quite irritating q:

I'm on a MBP Retina early 2013 15'

Does anybody have the slightest clue what's going on here? It happens often enough that hard resetting every time is not a viable long term solution.

Also, I'd be extremely useful to know what to do when this happens on other machines with other apps (:

I hope someone can help

Thanks Marco