The hosts were leading 1-0 when their full-back Kieran Gibbs appeared fortunate not to be sent off by referee Mark Clattenburg for a last-man foul on Hull winger Lazar Markovic 10 minutes into the second half which angered Hull.
"It is alleged that in or around the 55th minute of the game... the club failed to ensure that its players conducted themselves in an orderly fashion," English soccer's governing body said in a statement
Arsenal forward Alexis Sanchez had put the hosts ahead after 34 minutes when the ball inadvertently went into the net off the Chilean's hand after a goal-line save by keeper Eldin Jakupovic.
Sanchez added the second with a penalty in added time.
Hull have until Friday to respond to the charge.
(Reporting by Alan Baldwin, editing by Ken Ferris)
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