It's only happened about four or five times but when I have opened a video file, the main video window and the playlist window seem to have disappeared.
I spent ages trying to work out what had happened - I selected them in the VLC Window menu but nothing happened.
Then, I discovered that they were both at the bottom right of the screen with only a few pixels of the top left corner visible.
I thought it was a quirk of my Mac until it happened on my girlfriend's Mac a few days ago.
both are latest version: 2.0.5