Aaron Wilbraham cancelled out Billy Paynter's opener for Swindon, who dominated for large portions of the game at the County Ground.
Di Matteo's Dons also had Dean Lewington dismissed for incurring two yellows late on to compound their disappointment as they lost further ground on league-leaders Leicester.
"We fought well and created some chances from set-pieces but Swindon put us under pressure and although we got back into the game they gave us a bigger test than many other teams this season," said Di Matteo.
"We should have had a penalty when Luke Chadwick's shot was charged down but we are not getting those decisions. But we just have to play our football and get on with it.
"Dean Lewington was booked for arguing with the referee and then his second was for a challenge which was a little late."