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This has happened to multiple applications so far, i'm not sure what causes it, but it seems to happen after force quitting (sometimes).
First, you force quit it, and it does, but the dock shows that it is still open, but not responding. If you go to activity monitor, it does not show up. When you try to use the killall command by name, it tells you "No matching processes belonging to you were found". If you drag the file location into terminal, it still does not work. Deleting (using the rm command, as moving to trash does not work as finder claims the application is running) and reinstalling does not do anything, so i believe it has to do with the dock, or something else on the mac, not the application itself.
OS X Yosemite Version 10.10.3
My guess as to what might've happened is the application quit, but the computer never got any indication that it did for whatever reason, so telling it to quit does nothing, but you're not allowed to open an already open application, so you can't open or close it.
Things that do not work:
tell application "(application name)" to activate
Finder Menu : Relaunch