Manchester City midfielder Barry is serving a one-match suspension after admitting using insulting language towards Clattenburg during last Sunday's derby defeat to Manchester United.
However, Mancini has questioned whether Clattenburg, who was the fourth official at the Etihad, is taking a hardline stance after being forced out of the game for a month while being investigated for claims he used racist language towards Mikel.
Clattenburg was cleared of the allegations by police and the Football Association but still expressed concerns about his future in the game.
And Mancini said: "Gareth is a serious man, a serious player and I don't know why Clattenburg said these things about him.
"I don't know if it's because he had this problem after Chelsea but I think every referee or fourth official should understand if a player uses inappropriate words after they have lost a game in the last second.
"I don't know if he said those words against Chelsea players. They decided not but this is another situation.
"This has come from Clattenburg. He should understand the situation, that is my opinion, but at the moment he doesn't understand."
Don't miss any live and exclusive football coverage this festive season. Click here to visit Sky Sports' Festive Calendar