Stevenage's request to postpone their League Two match against Oldham in November because of international call-ups has been referred to an independent disciplinary commission by the EFL.
The postponement policy allows games to be called off if three players are selected for international duty.
But it has been alleged only two players were eligible to be counted.
Chairman Phil Wallace said he was "genuinely stunned" and the club said the complaint had come from Oldham.
Afghanistan's Noor Husin, Antigua, Barbuda defender Luther James-Wildin and Guyana's Terence Vancooten are the players in question.
Wallace added on the club website: "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."
An EFL statement read: "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 game, originally scheduled for 16 November, was played on 14 January, 2020.