The nail 'quicked' the hoof. It went into live, blood-supplied tissue and had to come out. Watch it for signs of lameness - it went into the blood supply and the 'hole' that the nail made goes from the bottom of the hoof upward, a route for infection. Since he has a shoe on, the chances of getting something stuck in there for infection are less, but that creeps me out.
Self-taught farriers can cut hooves and hammer nails, but that doesn't mean they are properly 'shoeing' the horse. The science of farriery is different than painting a house, you can't just see it and do it. The fact that he didn't have the guts or integrity to tell you that he quicked the horse is not a good sign - everybody knows about quicking, it's easy to do and even professional and trained farriers will do it on occasion, esp if the horse moves during that first strike of the hammer. Since he gave you a poofy story about stone bruises I wouldn't trust him. I have never heard of a stone bruise on the TOP of a hoof. Stone bruises are generally on the bottom or sole of the hoof. If your horse is lamed by him, you'll be out a lot more money than a good farrier would cost.