Stevenage have been referred to an independent disciplinary commission following the postponement of their scheduled League Two match against Oldham on November 16, the EFL has announced.
The fixture was rearranged under the international postponement policy after Stevenage had three players called up to represent their respective international teams.
Afghanistan's Noor Husin, Antigua and Barbuda defender Luther James-Wildin and Guyana's Terence Vancooten were the players in question.
But a statement from the EFL on Monday read: "The club had requested a postponement under the EFL 'postponement policy' which allows clubs to make an application in the event that three or more eligible players are called up to represent their respective national teams.
"However, following enquiries made by the EFL it is alleged that, at the time of the postponement request, only two players were eligible to be counted towards the total and not three as required by the policy.
"The fixture was subsequently played on 14 January, 2020. As this matter is now subject to proceedings, the EFL will be making no further comment at this time."
Stevenage chairman Phil Wallace revealed his shock at the news, telling the official club website: "We are genuinely stunned at the EFL's decision to refer their case to an Independent Disciplinary Committee.
"Our staff acted in good faith throughout and applied all the relevant rules available to us, making a legitimate postponement application which the EFL accepted and the FA subsequently reinforced by not allowing the player to play in our FA Cup replay.
"We have a 10-year unblemished record of administration in the EFL and will use the full resources at our disposal to support the decisions and actions of our staff in order to protect the reputation of the club and avoid the imposition of financial penalties."