VLC keeps freezing on Mac OS X El Capitan
You do not have the latest version of VLC for OS X, at the present time, the latest version of VLC for OS X is 2.2.2, so you might want to try it and see if the issue persists.

In clicking VLC > Check for Update..., note as shown in the image below it says:


  More than 100 fixes for issues reported for 2.2.1. 
  Full support of Mac OS X 10.11 El Capitan.




Note: If Check for Update... doesn't work then click the link above to download the vlc-2.2.2.dmg file and manually install it after deleting the existing application bundle.