WORLDGUARD-3205 - Reported by andrivard4

Using 5.9 this problem never occurred but using 6.0 beta 2 it seems that unless use is set to allow, any natural damage event (such as falling or burning) is not damaging the player.

Comment by sk89q

This is a known issue with beta 2. Please download the latest dev version as beta 3 is not yet out.

http://builds.enginehub.org/job/worldguard

It should fix your problem.