After last month's defeat Silva said Sam Barrott "didn't have the experience to handle the pressure".
Fulham striker Raul Jimenez was sent off and Silva unhappy no action was taken against Jamaal Lascelles when he caught the Mexican two minutes earlier.
The FA allege his comments constitute improper conduct.
In a statement, the FA said of Silva: "It is alleged that his comments in the post-match interviews following the fixture constitute improper conduct, in that they imply bias and/or question the integrity of and/or are insulting towards the match official and/or bring the game into disrepute."
Silva has until Monday, 8 January to respond.
-- Courtesy of BBC Sport