The Blues had lodged an official complaint against Clattenburg over inappropriate language allegedly used by the official after the two sides' league clash on Sunday.
Chelsea did not pursue claims that Juan Mata was also involved, with the Spaniard also featuring in the topsy-turvy Stamford Bridge clash.
Justifying why he played Mikel against Manchester United in Capital One match on Wednesday, Di Matteo added:“He’s [Mikel] fully focused on playing football. I wouldn’t have played him if I had any doubt.”
“I spoke to my players in the last couple of days and made sure they were in the right frame of mind to play, so I had no concerns in picking the team I wanted to," Di Matteo told reporters.
“First of all we had both midfield players booked in the first half and secondly I wanted to change a little bit the team tactically.
"They showed a big, big heart, passion and pride to not want to lose this game.
"It was a very exciting game of football to watch, a typical cup game, quite open at times, and a lot of mistakes from both teams because there were a lot of young players involved in the game.
“I’m very pleased with the players that I picked tonight. They performed on a big stage like tonight and they’re going to play an important role in our season.
“We are trying to change a little bit the way we play and at times you’re going to make mistakes.
"But young players will learn from it and get better from it, and as a team we will get better as well in not making mistakes. But that’s the way we want to go forward.”