I use hotwire maybe a few times a year and it has happened twice to me that the hotel they claimed was booked did not have the reservation. Most 3rd party booking sites don't have real time access to inventory, so if you book close to the same time that someone books direct, you can easily end up overbooked.

I think in the first case, they gave me a refund and I rebooked another through hotwire last minute. In the other case, the area was very booked up and I had to pay double to get a comparable room. So I had to send hotwire the invoice and they refunded the rate plus enough to cover the more expensive option. Both times was a huge inconvenience but that is sort of the price you pay for cheap 3rd party bookings.