Don't think about speed, but momentum. If you think that the fly is travelling one direction, at speed X, then hits the car, and is if then going the opposite way at speed Y, then yes, it implies at some point that the flies velocity must equal zero, and as it is in contact with the car, the car must also stop.

BUT, if you consider momentum, all you do is sum the momentum of the two objects, so;

MassCar x VelocityCar - MassFly x VelocityFly = post impact momentum.

Then divide the new momentum by the mass of the car, and you see how much the car actually slowed down.

Mart