Flanagan was punished by the SFA after the compliance officer deemed his elbow on Celtic captain Scott Brown - for which Flanagan was booked - to merit a further citation. The full-back will learn his fate after a hearing on Thursday.
Rangers have deemed the decision to be part of the “erosion of respect for Scotland’s referees” before also wondering why Simunovic wasn’t cited for a similar incident involving Jermain Defoe.
A club spokesperson told the Evening Times: “Once again, there seems intent to change the decision of a Referee in a match involving Rangers. There seems to be a steady erosion of respect for Scotland’s Referees and the authority they are meant to enjoy under Rule 5 of the Laws of the Game.
“The decisions of Referees regarding facts connected with play are meant to be final but Referees are now routinely invited to change their decisions after a game has finished.
“It is particularly shocking that another Rangers player has been singled out for retrospective action and issued with a notice of complaint while Jozo Simunovic, the Celtic player who used an elbow to fell Jermain Defoe, has escaped any kind of censure.
“Why did one incident escape punishment while the other is now deemed worthy of a red card? We cannot understand how these two incidents could be studied yet only one be considered worthy of punishment.
“It seems as if Rangers’ players are being held to a different code of conduct from players at other clubs. We shall vigorously defend Mr Flanagan and have also asked for full transparency on what matters are brought forward for retrospective action. Are those decisions being made even-handedly?”