Table-topping United recorded their tenth successive Premier League win as a second-half Cristiano Ronaldo free-kick earned the victory after Roque Santa Cruz had cancelled out Wayne Rooney's opener.
United, who were forced to work hard for the win, have now opened an eight-point lead over Liverpool ahead of the Reds' Sunday meeting with Manchester City, but Ferguson was more concerned with the behaviour of Pedersen.
The Norway international went down inside the United 18-yard area in the second half when touched by Rafael Da Silva and, after seeing Ronaldo booked earlier in the game for 'simulation', Ferguson was not impressed.
Question"The boy Pedersen dived," said Ferguson.
"There is no question about that at all. Yet Cristiano Ronaldo gets booked for the same thing and Pedersen doesn't.
"Both cases were the same. You have to give either a penalty or a yellow card."
Santa Cruz's goal was the first United have conceded in the league in 1,334 minutes, and Ferguson confesses his players could have defended better following a mix-up between Nani and Paul Scholes.
Injury headache"It was a really bad goal to give away," he added. "It was so soft and indicative of our performance really."
Meanwhile, Ferguson has an injury headache ahead of a mid-week UEFA Champions League meeting with Inter Milan.
Nemanja Vidic is suspended, while both Gary Neville and Wes Brown have been ruled out already, and now Ferguson seems certain to be without Jonny Evans, who limped off immediately after Ronaldo's winner.
Ferguson is now crossing his fingers that John O'Shea recovers from a sore heel in time to play against Jose Mourinho's side at the Giuseppe Meazza.
"It is a nightmare," added Ferguson. "Somewhere I have to find two centre-backs but it is looking very doubtful because Jonny is unlikely to play now."