No not the case at all. I booked the Westin Kaanapali Villas for one night and right after booking I call the Hotel and they see the reservation right away and add my Bonvoy#. Then I go online and see it like a normal reservation. I add my Mailing Address and Credit Card for Mobile Checkin and make any requests for views etc at the Hotel.
A mistake people make is not calling up the Vendor after booking well it could take a day or two to enter into the system but Hotwire is pretty good at showing up right away.
I would give it a day at most and call again if not press Hotwire for the reason and if they cannot honor the reservation have them switch you or g et a refund.