I had virtually the same thing with my current car. I had come of the scheme for a couple of years and was coming back on using my own car as a trade in. Collection day came and the car was sitting their, right colour, right spec so we did paperwork on mine and I entered pin and got in car only to find it was a manual!
Dealer checked and found error on his part so he immediately checked stock and found one arriving in 3 months but different colour. He phoned Motability and they sorted things out and he loaned me a new demo car until the new one arrived
All worked out but the payment from my Pip was dated from that day so my next payment was short. However, it was returned along with the full payment on month 2. Good side bonus was I got 3 months free car use.
It should be resolved as long as your dealer is helpful.