I have the same problem on my laptop with 16.04
CPU i5-6600
GPU HD 530

but the situation is fixed after canceled the option
"Accelerated video output(Overlay)"

in Preference > Video > Display

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which is subscribed to xserver-xorg-video-intel in Ubuntu.
https://bugs.launchpad.net/bugs/1537053

Title:
  vlc screen always on top, buggly.

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