I am currently dealing with this with Priceline. I booked a vacation bundle : car, hotel, flight. The charges came out in very odd ways on my card but no charge discrepancy so I kept the booking.
The rental car is through Thrifty. Which I do not recommend at all.
my stay is at Extended Stay. And even though I was charged by Priceline when I gave a card for incidentals it came through as a charge for the entire stay!
priceline is useless if you encounter any type of problem. I essentially paid for my rental car and hotel in addition to what I paid Priceline.