Rio Ferdinand starts a four-match ban on Sunday after a disciplinary panel ruled on Thursday that he had no basis to challenge the violent conduct charge brought against the Manchester United defender for his attack on Hull City's Craig Fagan at Old Trafford last week.
"There are conflicting ways in which these decisions are being viewed," said Ferguson.
"I watched the game between Leyton Orient and Charlton on Monday and there was an elbow on the Charlton player three times as he was running with the ball.
"But nothing has happened with that.
"There is a lot of confusion there, although we accept that Rio is banned."
Ferdinand was hit with an additional penalty, tagged on to the automatic three-game suspension, meaning he will miss the weekend blockbuster at Arsenal, plus Premier League games next month against Portsmouth, Aston Villa and Everton.
Although the decision was hardly a surprise as it seemed Ferguson had taken a calculated gamble to lodge an appeal that allowed Ferdinand to face Manchester City in Wednesday's Carling Cup semi-final.