Doncaster Rovers had been led to believe Wilks was available for selection despite picking up two yellow cards in earlier rounds and prepared throughout the week for him to start the game.
But after further checks were made by the club on Saturday, word came through in the evening that Wilks was indeed suspended for the tie.
It forced late changes to Rovers' approach to the game, which Rovers lost 2-0.
And while he would not use the disruption as an excuse for the defeat, McCann said it had not been
"It wasn't ideal to get a phonecall at half eight, nine o'clock on a Saturday night," McCann said.
"It's wires crossed somewhere.
"We've received an apology on it. We were led to believe he was okay to play.
"It disrupted us a bit. Everything had to change, the way we played, the set plays, things we had worked during the week.
"But that is not an excuse why we lost. We just got beat by a very, very good team.
"But I thought we matched them for long periods."
It is understood Wilks' name was not on a list of suspended players for the fifth round which Rovers had received from the Football Association earlier in the week.
But news of his availability had sparked concerns among members of the media and supporters who had interpreted FA regulations differently.
It was only with late pressing from Rovers on Saturday that the FA discovered their error - believed to be due to a clerical mistake by a match official in an earlier round.
"I got a phonecall last night and I think the media had been asking questions," McCann said.
"The FA explained to us in an email the reason for it but it's just one of those things."
McCann said Wilks accepted the news with good grace.
He said: "Mallik was all right. He was quite calm when I spoke to him on the phone last night.
"Probably the bigger disappointment was the players found out through Sky Sports New and it flashing up on there that he was suspended.
"That was the most disappointing thing but everyone makes mistakes and we move on.