The Manchester United manager said: "What I can't understand is the linesman's directly in front of it. He has no-one near him and he gets it wrong.
Related ArticlesManchester United 1 Chelsea 2Man Utd v Chelsea: as it happenedManchester United v Chelsea: match centreMan United v ChelseaPremier League tablePremier League fixtures"A game of that magnitude, you really need quality officials and we didn't get them today. It was a poor, poor performance."
Referee Mike Dean has been in the spotlight this week after Blackburn's Martin Olsson admitted he deliberately went down in the area at Burnley because of Dean's reputation for giving penalties.
United had two penalty appeals turned down today, while Chelsea also looked to have a good shout when Gary Neville barged Nicolas Anelka.
Asked whether Dean had been affected by the comments, Ferguson added: "I don't know about that but when I saw Mike Dean I did worry, I must admit."
Chelsea now lead United by two points with five games to go, and Ferguson put the pressure on his rivals by making them firm favourites.
"Five games left, they're two points ahead and four goals better than us - they're in the driving seat," he said.
"Chelsea are favourites now, there's no question. I'm certain we'll respond but we could win the next five games and not win it."
While United had a Champions League quarter-final against Bayern Munich to worry about in midweek, Chelsea were able to prepare solely for this game following their elimination by Inter Milan in the last round.
And both managers felt that proved a crucial factor.
Ferguson said: "The first half we looked leggy, it took us too long to get going and Chelsea were by far the better team.
"The second half we did well, we were unfortunate not to get something from the game. We dominated it in the second period but we just didn't get there."
Ancelotti added: "We kept a high intensity in the first half. We had good control of the game. We trained very well during the week because we didn't have a Champions League match. You lose a lot of energy.
"We played very well in the first half. It's a very important victory for us and a very important performance. To win here is not easy, we did a good job."
The Italian chose to leave Drogba out of the starting line-up and stick with the side that beat Aston Villa 7-1 last week.
Ancelotti said: "It was very tough to take out Didier but he understood because he trained not 100 per cent during the week.
"I preferred to put him on during the match and he did very well because he was fresh and he scored a fantastic goal."
Regarding his team's title chances, Ancelotti added: "We are favourites, it's normal, we are back at the top of the league.
"There are five games left and we have to stay focused. We are happy but nothing is decided so we must stay calm and focused on our game.
"(It's been a) good reaction after the defeat against Inter. My players are strong."
Chelsea winger Florent Malouda, who set up Cole's opener and caused United trouble all game, insisted the Blues are not taking anything for granted.
"It is going to be very difficult," he said of their title aspirations, on Sky Sports. "If we play the way we played today, we have a big possibility but it's going to be very, very hard.
"We wanted to be on top of the league after this game. It was hard but I think we played really well and for us it means a lot after the bad week we had. We had to react and we reacted in the best way."