Exactly this!

The reservation system is NOT coupled to the rental management system!

These days, reservation systems are largely automated (an automated system shops the competition and updates the rates based on what it finds out). However, while the reservation system is programmed with certain parameters that determine rates and availability, those parameters are input MANUALLY by an analyst who should be checking the actual inventory in the rental management system to make sure the parameters are keeping things on track.

If a parameter in the reservation system is set incorrectly or was overlooked by the analyst, the reservation system has NO WAY of knowing that the actual rental inventory is negative. A glitch can leave the flood gates open and hundreds of reservations can flow in for cars that don't exist.

The rest of jaguar1's post is 100% accurate, too. Rental rate management is an art, not a science. At a station with at least 500 or so cars (which is most every jet-serviced airport in the U.S.), vehicle availability is very fluid, since cars are coming and going all the time (often--actually, usually--not at all when they are expected to, since no one ever picks up or returns their cars on time). Within even just a few minutes, a dozen or so cars can be returned, taken through the wash, and placed out on the ready line. If you happen to be there 5 minutes before that, then you might think you're sunk; show up 5 minutes later and there's no wait for a car.

That all said, if the rental company doesn't have your car, then (as illustrated in this thread) it is entirely a fair expectation to be taken care of through whatever means necessary at a minimum of hassle and no additional cost to you.