I noticed this too. It's because the VLC volume slider goes up to 200%. In quicktime, if you go to movie properties and audio settings, it lets you increase volume to plus 6dB. Unfortunately because you changed the movie, it asks if you want to save it when you close it.
I don't know why volume sliders don't all go to 200%. It's a very useful feature, especially given that my Mac Mini has such a crummy built-in speaker.