Middlesbrough have been charged with failing to control their players in Sunday's Premier League match at the Riverside.
The Football Association charge relates to an incident around the 66th minute of the 2-2 draw against Manchester City.
The club "failed to ensure that its players conducted themselves in an orderly fashion", the FA said.
The club have until 18:00 BST on 5 May to respond to the charge.
Referee Kevin Friend awarded City a penalty for Marten de Roon's challenge on Leroy Sane. There was minimal contact as Sane appeared to run into De Roon's standing leg.