The match was played in a tense atmosphere, United having denied a report earlier in the day that Mourinho would be sacked that weekend regardless of the result.
"Luke Shaw is close to signing a new five-year contract at Manchester United worth £160,000-a-week".
It is alleged the 55-year-old used "abusive, insulting or improper language" following United's 3-2 comeback win at Old Trafford.
The United manager spoke into a camera after his side came from behind to triumph 3-2 at Old Trafford.
Mourinho could received a fine or a potential touchline ban if he's found guilty by the FA, and this isn't the first time the current United manager has been in trouble with the FA.
Spike reported nationwide in cases of baffling paralysis in children
Symptoms of AFM are similar to a severe respiratory illness along with a fever, but those progress into neurological symptoms. The condition is not new, but officials started to see a rise in cases in 2014; and there was another spike in 2016.
Mourinho has until Friday to respond to the charge.
Television cameras captured Mourinho muttering what are purported to have been "abusive and/or insulting and/or improper" remarks.
If Mourinho gets banned, it will be a double blow for Manchester United ahead of their clash against Chelsea, who are unbeaten in the English Premier League so far.