Oliver, the same referee who was surrounded by Manchester United players in the fractious FA Cup quarter-final with Chelsea last week and resulted in the club being fined �20,000 (23,000 euros, $24,700), awarded a penalty to Liverpool when he judged Gael Clichy to have fouled Roberto Firmino in the 50th minute.
"It is alleged that in or around the 50th minute of the fixture, the club failed to ensure its players conducted themselves in an orderly fashion," said an FA statement.
James Milner tucked away the penalty to give the visitors the lead but Sergio Aguero levelled with just over 20 minutes remaining to ensure City salvaged a point in the gripping match at Etihad Stadium.
Oliver booked both Clichy and his Spanish team-mate David Silva -- who was the most forthright in protesting -- after awarding the penalty.
City have until 1800GMT on Thursday to respond to the charge.