It is understood, however, the FA are not planning to take any action against the United manager as he did not question the referee's integrity or claim there was any bias.
Related ArticlesChelsea 1 Manchester United 0The Daily Bung: at least John Terry's appreciated at work.Carlo Ancelotti unhappy with United protestsAlan Hansen: Do not write United offUnited need to unleash Michael OwenJohn Terry shows character again"You lose faith in the refereeing sometimes that's the way the players are talking in there," said Ferguson, who felt Chelsea's winning goal should have been disallowed.
Atkinson awarded a free-kick for Darren Fletcher's challenge on Ashley Cole and Wes Brown appeared to be impeded as Frank Lampard's delivery was turned into the net by John Terry.
Ferguson said afterwards: "Clearly, Darren Fletcher's won the ball - Ashley Cole's never touched and has jumped up in the air - and then (Didier) Drogba's pulled Brown to the ground for the goal.
"The referee's position to make the decision was absolutely ridiculous - he can't see anything. He's got a Chelsea player (Joe Cole) standing right in front of him - and he doesn't even move.
"It was a bad decision, but there's nothing we can do about it. You lose faith in refereeing sometimes, that's the way the players are talking in there - it was a bad one."
The United players had protested when Terry's header glanced off Nicolas Anelka and beyond Edwin van der Sar for Chelsea's winner and there were also appeals for a first-half penalty when Antonio Valencia tangled with Terry.
As Wayne Rooney left the field, he mouthed the words "12 men" into the TV camera and could face an FA charge. Although he did not swear, Rooney's outburst will evoke comparisons with Didier Drogba's infamous rant after the Champions League semi-final against Barcelona that prompted a three-match Uefa ban.
"I think that the United players protested a lot, I don't know why I don't like this," said Carlo Ancelotti, the Chelsea manager.