I like Ville Niemi's approach best; ideally, to really humiliate Bob, Alice needs a setup where it's not obvious she's punking him. Reversing the steering, even the pedals, will make it obvious as soon as she starts driving that she's set him up, and that just proves to a guy like Bob that he was right all along. To really make Bob doubt himself, Alice needs a setup that she can drive exactly the same way Bob tried to, and works for her but not him.
First off, this needs to be a car Bob wants to drive. A pink Hello Kitty Smart Car, Bob will happily let Alice tool that around town by herself. A Mercedes E- or S-class, or anything else sufficiently manly and sophisticated, Bob will insist on driving that whenever they're going somewhere together. In addition, the car must appear to be stock; a car that's too obviously customized might give the game away, even if it's purely cosmetic.
The simplest thing I can think of is a button or switch out of sight that Alice can toggle discreetly (or that's built into the seat and reacts to change in body weight), that will change the behavior of the engine control computer (practically all fuel-injected cars of the last 30 years or so have had some sort of computer control). The behavior could be adjusted to make the car idle smoothly but stall when Bob presses on the gas, or revs past some fairly low limit that makes Bob have to drive the car like an old lady. When Alice drives, of course, she has none of these problems (but she should avoid showing off as that gives the game away that the car's letting Alice do things it won't allow Bob to do).
If it's a fairly new car, you could even use the 4G wireless capability of some new models to let Alice hack in through a phone or laptop when she's not riding with Bob. She could do any host of things; kill the motor, cut the power steering, turn on the check engine light (and then have a mechanic in the know give a horrific figure to repair that Alice then makes Bob pay because "it only breaks down when you drive it, it's been fine for me, you must be driving it too hard"), etc. The mechanics could take Bob's money and sneak it to Alice on the sly, maybe with a cut for them to sweeten the whole deal.
Eventually, Bob's inability to drive Alice's car "properly", and the resulting paranoia that somehow Alice's car is out to get him, becomes an indivisible rift in the relationship, and she breaks up with him because she can't be with a guy that's so hung up on a (censored) car.