The /refer command is understandably confusing to players, as it should be used by the player being referred, not the player doing the referring. It would be much less confusing with something like this:

• Change the /refer command to a 2-step referral system
  • Player A invites player B to the server
  • Player A uses the /refer command on Player B
  • Player B is sent a message about the referral, and runs a command (ie; /confirm) to confirm that player A referred them

This would make the referral system so much easier to understand for players.