Mathias Doumbe's 58th-minute header and substitute Ryan Lowe's cool last-minute finish handed the in-form Dons their third win in four games, leaving the Robins without a win in four.
MacDonald said: "It's very disappointing that we've lost 2-0, especially as we felt we outplayed them in the first half.
"In games like these, big decisions by the officials can certainly change matches and I didn't see anything wrong with our goal - the referee was only five yards away and the linesman on the touchline sees it.
"I was disappointed with the second half, from a set-play we got done and we've got some big players in there.
"Probably by the letter of the law he could have sent (goalkeeper) Wes (Foderingham) off.
"That was the wrong decision by Wes in many ways but then I felt the referee got the decision wrong at the other end as well - but two bad decisions don't make it right.
"We've just got to get down on the training ground and work hard together to get back to winning ways.
"Everybody has always been looking over their shoulders but we've got to get on with it and look to get 12 points."