Sometimes horses yawn when you are teaching them stuff, particularly groundwork and especially when they have to think! If he does it during this I would take it as a sign to stop for the day. Alternatively he could just be tired!
I had one once who had clicked his jaw or something - can't remember the details, it was a long time ago, but it was a vet job. He was an Arab. Mind you, that was absolutely compulsive, he yawned all day. Used to set me off