I had a similar problem in December. I had left the scheme but had decided to rejoin and ordered a Mazda CX5 auto in November with deliver mid December. Traded my car in against the AP.
Arrived to collect my car, did the paperwork and signed over my personal car. Dealer went to bring the car round and came back to me saying the car was manual. Checked order and found he had ticked the wrong box!
He couldn’t have been more apologetic or helpful. Cancelled the order, ordered a replacement car arriving late January, took care of all the paperwork with Motability and gave us a demonstrator car until the new one arrived.
All depends on the service levels of the dealer.