I don't think the refs should be involved in accepting or declining a coaches challenge. If a coach wants to throw a red flag, let him. It ain't the refs problem if the coach don't know the rules. The ref should come over to the coach on the sideline and ask, "What are you challenging?" The coach tells him, and the ref should do an about face and go straight to the review booth not saying anything more to the coach, even if the coach has questions about the play.
In this scenairo, we would surely find who the dumbest coaches are in the league!
