Rotherham have been charged with fielding an ineligible player in their Championship meeting with Brighton on Easter Monday.
On-loan defender Farrend Rawson played 90 minutes in the Millers' 1-0 win and boss Steve Evans claimed after the game that the Derby man's youth loan had been extended until the end of the season.
But Rawson was not involved in Rotherham's 2-0 defeat at Middlesbrough on Saturday, with Evans adding to the confusion afterwards by saying he had been recalled by the Rams.
The case will now be heard by a disciplinary panel who hope to rule on the matter before the end of the season.
A Football League statement read: "The Football League has charged Rotherham United with fielding an ineligible player [Farrend Rawson] in the club's Championship match with Brighton & Hove Albion on Monday, April 6 which the Millers won 1-0.
"The matter will be heard by a Football Disciplinary Commission (FDC) which will take place at the earliest possible opportunity to ensure that it reaches its conclusion before the end of the current season."
A Rotherham statement added: "Rotherham United FC have received a charge in relation to fielding an unregistered player.
"The case will be heard before the FDC and such proceedings under league rules are confidential until the case is concluded.
"Therefore we have been advised by our counsel Jim Sturman QC to make no further comment until the case is concluded."
The Millers, in their first season in the Championship following back-to-back promotions, are currently seven points above the relegation zone with four games to play.