We had a kitten who did that for months. She was loosing her baby teeth and chewing on them as they were coming out. Another kitten had the habit of just grinding his teeth when stressed. Our girl Wookie (RIP) did it when she ate because half of her face was paralized and she just couldn't eat right on that side of her mouth and would, basically, chew on her teeth as she ate her food.
How old is your kitten? Is it possible he's just loosing his baby teeth? That would be my first thought.