In the 37th minute of the 3-3 draw at Brunton Park, Miller went down easily under a challenge from Daniel Scarr inside the penalty area, leading to venomous protests from many of the Wycombe players.
A spot kick was awarded and converted, before Wycombe fought back to claim a 3-3 draw in the League Two fixture, but the FA has chosen to punish Miller after replays suggested that there had been little contact.
A statement read: "Incidents which suggest a match official has been deceived by an act of simulation are referred to a panel consisting of one ex-match official, one ex-manager and one ex-player.
"Each panel member will be asked to review all available video footage independently of one another to determine whether they consider it was an offence of 'successful deception of a match official'.
"Only in circumstances where the panel are unanimous would the FA issue a charge."
Miller - who has scored once in 13 games at the fourth tier this season - has until 6pm on Thursday, October 19 to appeal the charge.