Rafael, Jonny Evans, Antonio Valencia, Phil Jones and Robin van Persie were all shown yellow cards at the Emirates Stadium which Ferguson felt was a bit excessive, especially after the Gunners began in such an aggressive fashion.
"Arsenal set off at a fantastic pace, very aggressive and a lot of tackles," Fergie told Sky Sports.
"The referee just could not keep up at that point. When we had a foul, he booked us straight away. We had five players booked.
"We have got probably the best disciplinary record in the country. For Manchester United to have five players booked, I do not think that is right."
Ferguson, however, felt his side could have achieved victory if they were more efficient in front of goal.
"We expected a tough game and we got a tough game. Arsenal are fighting for the Champions League. We expected a real challenge," he added.
"But, in fairness to the players, once we had scored, if they had taken one or two of their chances, I think we would have won quite comfortably."