How to quit an app in OS X Yosemite

I have this annoying BitTorrent app that won't quit. I first tried right clicking and force quit from dock. It does show 'App not responding', however, on clicking 'Force quit' nothing happens, and the app persists in the dock with the black dot below:

So I next opened 'Force Quit' from Apple menu, and clicking it launches the list of processes open, and sure there I see BitTorrent. However, same here, on force quitting it, nothing happens, the app name is still there in the list of open apps.

So I next open Activity monitor, and check if it is there. However, as you can see, it is not there:

However, if I switch to the energy tab, I see BitTorrent there, but it shows as disabled, and consequently I am unable to quit it by clicking the cancel button at the top left (which is disabled):

So I login to my terminal, and type top to see whether the app shows up, and it doesn't.

Then I try launchctl list to see which things were launched by Apple at startup, and spot something like com.bittorrent.BitTorrent.307036. So I run sudo launchctl remove com.bittorrent.BitTorrent.307036, and still nothing happens, the app remains frozen in the dock.

Finally, I tried killall dock and it does nothing. This is happening quite frequently off late. Last day it happened to my Outlook app, I had to restart to get rid of it. How do I solve this problem?