Fulham coach Marco Silva was also charged by the FA on Monday.
During the second half of Sunday's tie, a confrontation broke out after Fulham's Willian was red-carded for handling the ball in the box following a VAR review.
During a chaotic few minutes, coach Silva angrily addressed the fourth official before being shown a red card.
Serbian forward Mitrovic was also red-carded after confronting referee Chris Kavanagh and shoving him with his shoulder.
"It's alleged that Marco Silva used abusive and/or insulting words, and/or gestures and/or behaviours towards the fourth official prior to his dismissal and after being sent off," the FA said in a statement.
"It's further alleged that in throwing a water bottle in the direction of the assistant referee his behaviour was improper."
The FA also said that Mitrovic's behaviour after the sending off was insulting and threatening.
"The standard punishment which would otherwise apply to Aleksander Mitrovic for the sending off offence of violent conduct that he committed towards the match referee is clearly insufficient."
The governing body added that Fulham failed to ensure that their players would behave themselves and has yet to announce the sanctions to be handed down.
