I have it in the bukkit forum. Its very easy bug fix. As explained in the following link that the API method "permission.getPrimaryGroup()" does not work. It is better explained here.

http://forums.bukkit.org/threads/this-is-information-on-vault-bug.96919/

You don't say which permission plugin you're using..

Sorry about that I added it when someone asked, its pex

looks like this will need to be resolved in PEX as it doesn't sort properly in certain circumstances.