The Pilgrims’ head coach faces three charges related to the incident, which occurred after Joe Rankin-Costello scored the visitors’ equalizer in the 87th minute.
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Plymouth believed there was a foul on Ryan Hardie in the lead-up to the goal.
Rooney is accused of using insulting or abusive language toward a match official and of displaying improper and/or violent conduct after receiving the red card.
He also faces an additional charge for returning to the pitch following his dismissal.
Plymouth secured the win with a stoppage-time header from Morgan Whittaker.
Rooney’s assistant, Pete Shuttleworth, remarked that the former England captain’s “passion” led to the incident.
Rooney, who has been in charge of Argyle since May, has until Tuesday, October 15, to respond to the charges.
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