The Red Devils boss is angered that Bolton Wanderers' Zat Knight didn't see red for his challenge on Danny Welbeck, which gave the Premier League champions a penalty during their 3-0 win over Owen Coyle's side on Saturday.
"We should have been playing against 10 men," said Ferguson. "But these inconsistencies are confusing to everyone. Referees have to be given direction about what are the laws of the game and what should be permitted in terms of tackles.
"[Referees' chief] Mike Riley has to be given the rope to say this is not allowed, two-footed tackles are not acceptable, whether you take the ball or not."
Refereeing decisions have made the headlines recently following a controversial red card against Manchester City's Vincent Kompany, which resulted in a four-match ban for the City captain.