Ferguson says Michael Essien fouled Ryan Giggs in extra time and stopped the veteran winger from having a chance on goal and should have been awarded a penalty.
Ferguson said: “It’s a penalty. To lose a game and see that is disappointing.
“I think the pressure Jose Mourinho put on the referee before the game has certainly worked and I’m disappointed at that.”
Chelsea keeper Petr Cech appeared to carry the ball over the line on Giggs’ effort.
Ferguson added: “It’s a penalty kick. Then the goalkeeper’s spilled the ball behind the line.
“I think it would have been a difficult one for the linesman to call but the referee should be in a better position.
“We couldn’t see where we were but when I see it now it’s a penalty.”