Ferguson was not happy with Nigel De Jong's challenge on Danny Welbeck, nor the manner in which Mancini was talking to fourth official Jones.
Jones stood between the pair at one point during the row to prevent it spilling over before they were eventually pulled apart by members of their respective backroom teams.
"He refereed the game," said Ferguson.
"He was out on that touchline the whole game haranguing the referee, the fourth official and the linesmen.
"The minute I come off the bench for bad tackle by De Jong on Welbeck, he was out again.
"He can't have it both ways. He's been complaining about referees."