Di Matteo refused to comment on the Blues' allegations Mark Clattenburg used "inappropriate language" towards John Obi Mikel but hit out again at the official's performance in Sunday's loss at Stamford Bridge.
That result came barely a year after Chelsea also saw two men sent off in their derby defeat at QPR and became embroiled in a race row, similar to the one currently under Football Association and police investigation.
Complaining about decisions made against his side Di Matteo said: "It's incredible that it always hits Chelsea Football Club.
"So maybe that's something to think about, you know."
"We would just like to be treated fairly by everybody."
Asked after tonight's [Wednesday] 5-4 extra-time win if Chelsea had been treated unfairly, he replied: "I don't know."
Di Matteo insisted he was not worried about how Chelsea would be refereed after making their complaint against Clattenburg, who is understood to deny any wrongdoing.
"I think the referees should be going into the games with the most confidence that they have," he said.
"We're all under pressure here - the players, the officials, the coaching staff - to perform.
"And I don't think there's any prejudice from that point of view."
Chelsea fell behind three times tonight [Wednesday] but came roaring back each time, taking the game to extra-time with a penalty that was the last kick of normal time.
The European champions twice came from behind before losing on Sunday as well.
Di Matteo said: "I think we showed on Sunday already that we've got big characters in the dressing room and we had to show it again tonight.
"They showed a big, big heart and passion and pride to not want to lose this game.
"It was a very exciting game of football to watch, typical cup game, quite open at times and a lot of mistakes from both teams because there were probably a lot of young players involved in this game."
Di Matteo opted to start with Mikel and Juan Mata, despite them being at the centre of the Clattenburg affair.
"I spoke to my players in the last couple of days and, mentally, they were in the right frame of mind to play," he said.
Di Matteo withdrew Mikel at half-time but insisted it was for tactical reasons and the fact the midfielder had been booked.
He added: "I wouldn't have played him if I had any doubt."
The Italian was missing key men tonight [Wednesday] through injury and suspension, including Ashley Cole, who has an ankle problem.
He said: "Hopefully, he'll be okay for Saturday. But I can't say yet."