The whole hotel booking site world is like a zoo. You've got booking sites doing deals with hotels, booking sites doing deals with bedbanks, booking sites that consolidate from other booking sites, possibly including other consolidators, and so ad infinitum. Over and above that is the suspicion that the hotel puts you in a crap room when you use a booking site.
I've never used Booking.com. As other commentards have pointed out, they rarely seem to be the cheapest, which makes this story rather surprising.