This is exactly what happened to me this weekend at the Residence Inn Downtown Toronto. I had originally booked a one night stay, but later added a second. I've done this in the past with no problem. However, when I arrived at the hotel, it showed up in the computer as two different reservations. Not a big deal, but I had to go change my key cards the next day. I checked my account while I was there and there were two charges for the hold. One for $258 and the other for $155. I'm usually on a tight budget when I travel, but thankfully this didn't have an effect on my trip. I wish I was given a heads up when checking in, but that is my fault for not asking when they took my card.
