From USA Today:

Despite its success at boosting demand for fuel-efficient vehicles, the cash-for-clunkers program has been riddled with problems since the start. Days after its debut, the program almost ran out of money. An additional $2 billion was added to the pot. But many dealers say they still haven’t been paid back for cars they’ve sold with the clunker discount.
Customers heading out to dealers this weekend will find that many car lots are out of vehicles that qualify for the program. And if cars are available, be wary of the grumpy salesperson: Dealers say their salespeople aren’t all that motivated to spend hours scanning in papers, faxing them to the government, then dealing with technicalities that crop up once the government starts sifting through the paperwork.
“It’s a quagmire,” says George Fowler, general manager of Superior Pontiac Buick GMC in Dearborn, Mich. “These aren’t cars we traditionally make a lot of money on. It’s a ridiculous amount of work, and my guys are making $100 per car.”