Earlier on, referee Steve Bennett had sent off Didier Zokora for a two-footed challenge but only booked Steed Malbranque for a similar tackle a few minutes later - and the Frenchman twisted the knife by adding the second goal late on.
Dunne told City's website: "It was one of those that if it had been me I would have thought I would have given away a penalty. Nine times out of ten it should have been given, the referee has missed it and it has probably cost us in the end.
"What can we do? It was a penalty, but the referee has not seen it, he said I ran straight into him.
"We've seen all the incidents afterwards on the laptop, and they all seem wrong. There are bookings when there should not have been and red cards when they should have been bookings, it was one of those nights for everybody I suppose. We did not have a good night and neither did the referee really."