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?

(I know this is an old question but I think this might help somebody)

I had the same problem with NetBeans and this is what worked for me:

sudo killall launchservicesd
sudo killall Dock

I hope this helps.

I'm running OS X 10.11 "El Capitan" on my Macbook Pro, and I'm experiencing this issue with Mozilla Firefox. Unfortunately, in my case the commands sudo killall launchservicesd and sudo killall Dock aren't working this problem out: after I do this, I still can't e.g. reboot the operating system.

I found that the following command works on Macs:

sudo shutdown -r now

If your user account has administrative privileges on OS X, running the above command on Terminal will force OS X to reboot. Unfortunately, this is not a solution for the issue, but as a "last resource workaround" it works like a charm.

This is based on loco.loop's answer. This was happening to me very frequently with Synergy app. I've now turned this into a bash script.

sudo echo "#!/bin/bash
sudo killall launchservicesd
sudo killall Dock" > /usr/local/bin/fixDock && sudo chmod +x  
/usr/local/bin/fixDock

Now I just type fixDock in my terminal. :)