To get bitten during feeding is not rare at all. It happens when owners do not think before they put their hand in the range of their snake. I do agree that removing your snake from its enclosure is not necessary, but some owners do do it.
To the OP, if you are concerned in the future about feeding and your snake consuming substrate, you can put a piece of newspaper over the substrate where you put the prey, but this does not usually help for feeding live because the prey can go where ever it pleases. If you do become concerned about your bp consuming substrate on a regular basis, unprinted newspaper may be better to use rather then substrate. I personally use Scott Shop Towels, because they are not as unsightly as printed newspaper, VERY thick and absorbent, and easy to clean.