How common? In some 20 years of staying at Hiltons and using amex, I've never had this happen. But see:
Double charged (adv. purchase and checkout)
Prepaid rates aren't always charged at the time of booking (even though one would think that they should be, that is what prepaid means to me); this is especially common with non-USA properties.
Prepayment for Hilton Not Showing up on Credit Card??