I too have had this happen before. A few scales were missing off of my '02 male, from the top of his head between the eyes, after one of his sheds last year. I looked at the shed skin (which came off in one piece) and you could actually see the missing scales stuck to the skin.
I know that before a shed, fluid builds up between the new skin, and the old one. I have read that if a snake is dehydrated or has not been drinking water enough before a shed, this fluid will not be present in a good-enough amount to make the shed go smoothly. In my snake's case, I had been away and came home to find him "in the blue" and I upped his humidity, but not soon enough.
I'd make sure that fresh, unheated drinking water is available at all times, changed daily. And also remember to "up" the humidity as soon as the snake's eyes go blue. Doing these things should ensure that the snake is hydrated enough for its next shed.
Incidentally, the snake I was talking about is doing great today. If you look closely, the scales on his head never did grow back, but the white spaces turned dark and never did get infected. I had put neosporin on the missing-scale spots for a few days to prevent infection.
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2.1 Ball pythons
1.0 Boa Constrictor Imperator
0.1 huge fat albino Cranwell's horned frog
etc..