Being insomniac very often, I have the habit of watching series or movies at night. And as I often fell asleep in the middle, I use the OSX scheduled shutdown to avoid my Mac of running all night for nothing. But each morning, I have the same message saying that the shutdown couldn't be made because of VLC not quitting...
I was curious about it, as I usually have no problem to quit VLC, so I tried a scheduled shutdown during the day to see what's going on. And to my surprise, at the moment OSX is going to shut down, VLC doesn't do anything during 1 to 2 minutes before quitting, long enough to disable the shutdown... And during another test, I've seen that just moving the mouse a little during this couple of minutes seems to awake VLC and then it decides to quit for real... What the ?...
For the note, I remember having the exact same problem some years ago under Leopard and Snow Leopard (now on Mountain Lion).