Fulham manager Marco Silva has been charged with misconduct for his comments following the 3-1 FA Cup quarter-final defeat to Manchester United earlier this month.
The West London club took the lead in the FA Cup tie through Aleksandar Mitrovic, but a minute of madness turned the game on its head.
Man United were awarded a penalty following a VAR review, which resulted in Willian being shown a red card for a deliberate handball on the goalline.
Mitrovic was also given his marching orders for pushing referee Chris Kavanagh, while Silva was sent to the stands for his actions when the official went to the monitor.
Speaking to reporters after the game, Silva said: "Our story with Chris Kavanagh this season has been tough for us.
"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."
Silva had previously been charged with abusive behaviour towards the match official, and the Football Association has now issued another charge of misconduct for his post-match comments.
The FA alleges that Silva's comments following the FA Cup defeat "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 Fulham boss, who now has until March 29 to provide a response, is also facing the prospect of an improper conduct charge for allegedly throwing a water bottle in the direction of the assistant referee.
Mitrovic has already been charged with improper conduct, and he could be handed a lengthy ban for his actions.
Man United were unable to escape the situation unscathed after they were hit with an FA charge for allegedly failing to control their players during the 71st-minute incident. body check tags ::
