Why was the vehicle Neil rented not there?

yes

It had to have been a screw up on the part of Marathon. It's been hypothesized that Del got the car but that's not true, the car the shuttle driver told Neal would be in V5 is not the car that Del is driving (he's in the family truckster, not a white Lincoln). Plus when Neal is punched by the cab driver Del had just gotten the family truckster, Neal would have beaten him to the car.

The rental company just screwed up.

All he had to do was keep calm, maintain his reservation ticket, and he would’ve received another car