Manchester City players surround referee Simon Hooper
Players surrounded referee Simon Hooper when he awarded a free-kick to City late in stoppage time after it looked like Jack Grealish was through on goal.
Hooper initially indicated City had the advantage and waved play on, but halted the match once the pass was played.
City have until Thursday, 7 December to respond to the charge.
An FA statement said the defending champions "failed to ensure their players do not behave in a way which is improper."
Striker Erling Haaland was one of several City players to remonstrate with the official and he continued his protests after the game by reposting a clip of the incident on X, formerly Twitter, with the comment "Wtf", which is offensive slang.
However, the FA will not be handing out any further charges relating to the fixture, so Haaland is not facing an individual punishment.
It is the third Premier League game in succession that City have drawn, having also been held by Liverpool and Chelsea, and they sit third in the Premier League with a three-point gap to leaders Arsenal.
-- Courtesy of BBC Sport