London strategist Andre Villas Boas complained about referee Howard Webb's work after a draw.
The capital team took a 3-0 lead, but wasted the advantage in less than 40 minutes of the second half. The referee also contributed to this by awarding two penalty kicks.
"The first episode definitely deserved a penalty, there is nothing to add, but the second one is very questionable," said Villas Boas. "I don't know if Webb was in the right position to make such a decision. Danny Welbeck's foot simply caught Branislav Ivanovic."
He continued: "I don't know if the referee was trying to compensate for the mistakes made in the first half, but he made a mistake in this episode. We hope that the best referees will officiate in the most important matches, but that wasn't the case. In Manchester, opponents scored two goals from offside, now controversy cannot be avoided."
Meanwhile, Manchester United manager Sir Alex Ferguson said: "We played better than our opponents for 80 minutes, but immediately after the break we conceded two goals in just a few minutes, it was a big blow. I think Gary Cahill should have been sent off the field in the first half for stopping a dangerous attack. I don't blame the referee, he should have been assisted by the linesman."