I've been getting these types of errors. They seem to come from new players on the server who are not in the users.yml although the errors do seem to show even after they have been added. Could this be caused by the "worlds: {}" attribute not being added to these players? With Privileges v1.1.0-b5 the worlds attribute is not added with the users like in previous versions.

[SEVERE] Could not pass event PLAYER_JOIN to Privileges
java.lang.NullPointerException
at net.krinsoft.privileges.PermissionManager.calculatePlayerPermissions(PermissionManager.java:174)
at net.krinsoft.privileges.PermissionManager.registerPlayer(PermissionManager.java:63)
at net.krinsoft.privileges.PlayerListener.onPlayerJoin(PlayerListener.java:24)

[SEVERE] Could not pass event PLAYER_PORTAL to Privileges
java.lang.NullPointerException
at net.krinsoft.privileges.PermissionManager.calculatePlayerPermissions(PermissionManager.java:174)
at net.krinsoft.privileges.PermissionManager.registerPlayer(PermissionManager.java:63)
at net.krinsoft.privileges.PermissionManager.updatePlayerWorld(PermissionManager.java:130)
at net.krinsoft.privileges.PlayerListener.onPlayerPortal(PlayerListener.java:47)

This should now be fixed, but your suspicions are correct; it's caused by the lack of a relevant world path being created for the players. I didn't realize the depth of the FileConfiguration class's depravity, I need to amend my Pull request. :[

Closed as of this commit.