The Millers will face a disciplinary commission after defender Farrend Rawson played 90 minutes in Easter Monday's 1-0 win over Brighton after his youth loan had expired.
The Football League is keen for the matter to be resolved before the end of the season which could impact on Rotherham's Sky Bet Championship survival hopes if they have points taken off them if found guilty.
Evans' men are currently seven points clear of the drop zone, but that will decrease after Tuesday night's clash between Millwall and Wigan - the two sides immediately below them in the table - with the South Yorkshire club not in action until they head to Fulham on Wednesday.
Evans, who absolved himself of any blame in the incident which led to the charge, said: "I was 100 per cent gobsmacked when I found out and the players were the same.
"We are not involved with things like loans and forms and contracts, we are here to pick the players and let other people do the administration side.
"That's all I know, so we have to just get on with it and let that process take place behind the scenes.
"I wasn't angry, we are together as a football club, we can only affect results on the pitch.
"We have to keep our focus on Fulham, on the four matches we have got left and let a process take place.
"It was always going to be an interesting end to the season. We were always going to be in that position, we have to keep our focus on the football.
"What I do 100 per cent believe that when it gets to the hearing it will be a full and fair for Rotherham United."
Asked if he thought a points deduction could see his side relegated, Evans added: "If we lose three points we're getting relegated? Behave yourself.
"That's not going to happen, we have got points to play for. We don't know if it's going to have anything to do with points, we have to let that process take its place, there is always two sides.
"All I know is that we have got 43 points on the board until anyone tells me differently.
"There is a lot of football to be played between now and the end of the season and I would suggest that will have more to do whether we are going to be a Championship club than the process the Football League are involved in.
"We have got 12 points to play for not three."