Are you sure they're missing scales? Or just discolored? My BP will occasionally have a small splotch or two of gray scales after a shed, usually on the head or neck area. It's totally random and always disappears after the next shed. And she's never had any difficulty with complete, clean sheds. Adam says its harmless.
If the scales ARE missing....I dunno. Maybe the snake got a little too enthusiastic about shedding and that part of the skin wasn't ready to let go of the old yet?