Silva had already been charged with abusive behavior towards the match officials after Willian and Aleksandr Mitrovic received red cards in quick succession.
Referee Chris Kavanagh bore the brunt of Silva after the game, with the Fulham boss alleging bias on the path of the official.
"Our story with Chris Kavanagh this season has been tough for us," said Silva after the game.
"Unfortunately, we have been very unlucky with him this season. Many moments. It is difficult to understand some of the decisions.
"We had that West Ham game away from home [in October]. We lost the game with two clear handball goals and it was Chris Kavanagh in that moment. Today, everyone saw what is happening in this game. It is difficult for them to not look for these things."
A statement from the FA read: "Fulham's Marco Silva has been charged with misconduct for comments that he made in a press conference after the FA Cup tie against Manchester United on Sunday 19 March.
"It's alleged that his comments constitute improper conduct in that they imply bias and/or question the integrity of the match official, and/or bring the game into disrepute.
"The manager has until Wednesday 29 March to provide his response."
