Referee Michael Oliver's decision to give the visitors a penalty at the Etihad Stadium was met with fierce protest from City players, who crowded round the match official.
James Milner nevertheless converted from the spot, before Sergio Aguero sealed a draw for his side 20 minutes from the end.
But as the FA confirmed on Monday, Pep Guardiola's men crossed the line in their protests and the club is now liable to pay a fine of £35,000.
"Following an Independent Regulatory Commission hearing today [Monday 27 March 2017], Manchester City have been fined £35,000 after the club admitted an FA misconduct charge," a statement read.
"City breached FA Rule E20(a) in that in or around the 50th minute of the game against Liverpool on 19 March 2017, the club failed to ensure that its players conducted themselves in an orderly fashion."