In a relatively even contest, Falkirk midfielder Arnau Riera was red-carded for a challenge on Andy Dorman minutes before the former New England Revolution midfielder scored the only goal of the game with a wonderful volley.
The Falkirk boss questioned the wisdom and motives of McVicar, who is the SFA's head of referee development and former FIFA referee Hugh Dallas, the SFA's referee development officer, for allowing MacDonald to referee his side in what was only his second SPL game of the season.
McVicar said that Hughes, who was called into MacDonald's room after the game after an exchange of words in the tunnel, should go through the correct channels to register his complaints and concerns.
He said: "John Hughes has never had any dialogue with us and has never asked for any dialogue.
"Therefore, it would be better if he addressed us rather than making his points through a third party."