I've had this happen more than once, where Amazon received my books twice, and like you, have had times where phantom copies sold.

Eventually, Amazon figured it out; usually the orders disappeared and inventory eventually went back to the correct numbers. Once I got reimbursed for all of the "lost" books (not that it was a windfall, but since they never existed anyway, I didn't complain).

Really nothing you can do about it. Amazon will eventually figure out that either they counted wrong, or that they lost it.