In order for them to file a 1099, they have to at a minimum your social security number. If you foolishly allowed the dealer to run your credit and finance your vehicle, they had that information.
If you financed the vehicle, you are much better in using the rebate to reduce the purchase price, and thus reduce the amount financed and saving the interest you would have paid on that amount. If you paid cash, there is literally no difference between getting the rebate money in your pocket or paying a lesser amount for the vehicle.
I am betting this is just an poorly informed finance "manager". If the entire rebate was taken off the purchase price, then you actually received the full benefit of the rebate. No harm, no foul.