The official sent off Fernando Torres for what he deemed a dive midway through the second half, with TV replays suggesting that Chicharito was offside when he scored the winner for the Red Devils. He had earlier also red-carded Branislav Ivanovic for a professional foul, though the Italian accepted that decision.
"The key decisions from the referee today influenced the result," the manager told Sky Sports. "He sent off Fernando Torres and the third goal is offside - those things have clearly decided the game in the favour of our opposition.
"Torres put the ball through Evans' legs, he's through and then gets kicked on the shin and goes down. It is as simple as that.
|22/1||Chelsea are 22/1 with William Hill to beat Manchester United 3-2 in the Capital One Cup
"I'e watched the replay of the third goal again and it's clear once Rafael shoots, Chicharito is in an offside position," Di Matteo added. "Everything went for United in that sense and that makes us unhappy.
"I have spoken to the referee. He will probably watch it again and realise he has made mistakes but we can't change the result now and that is the biggest disappointment for us.
"I've no complaints about the first sending-off. I think Ivanovic tried to get out of his way but just clipped his heel before Young went down."
Chelsea conceded twice in the first 12 minutes and Di Matteo admitted that they started poorly but was pleased with their response, bringing the score back to level terms before the red cards.
"We had a slow start to the game," he observed. "They were a bit lucky with the first goal that bounced off the post and onto David Luiz. With the second goal I think we defended badly.
"But then we had a great comeback and I thought the momentum had turned for us and that we were probably the most likely team to win the game. I think if we had just gone down to 10 men we would still have been able to cope but obviously the second sending-off made the game really difficult for us.
"I don't think we deserved to lose. When the game was even we showed how strong we are and I felt very confident we would go on to win the game, and even when we went down to 10, I didn’t think we were going to lose."