The horrific challenge during Sunday's 2-1 win for the Latics was not punished at the time, with referee Mark Halsey believed to have not seen the full extent of the incident.
It left Haidara with a potentially serious knee injury, and sparked ugly scenes at half-time as players and coaching staff from both sides confronted each other.
FA disciplinary officials will review all available video footage of the challenge and are also waiting for Halsey's report before making a decision.
Wigan's outspoken chairman Whelan insisted that McManaman was trying to win the ball, and that contact was accidental and not a result of the player losing control.
"The ball was there and McManaman got the ball as clear as a whistle, then followed through and they collided," Whelan told BBC Radio 5 live.
"He hasn't gone over the ball. That's an accident," added Whelan, whose own playing career was interrupted by a broken leg suffered in the 1960 FA Cup final.
"When I broke my leg in the cup final it was exactly the same type of tackle. We both went for the ball. It brought back memories. It ruined my career. I am not going to criticise Norman Deeley.
"These things happen in football. He came over the ball but he didn't do it with the aim of breaking my leg."
Usually, on-the-ball incidents cannot be dealt with retrospectively as it is seen as challenging the opinion of the referee.
If however, Halsey reports he did not see the studs-up lunge by McManaman because he was unsighted then the Wigan player could be charged.
Haidara suffered potential knee ligament damage and the incident resulted in Newcastle assistant manager John Carver and Wigan coach Graham Barrow being sent to the stands after a melee developed at the end of the first half.
Newcastle manager Alan Pardew claimed Halsey had said he had not seen the incident.
"He (Halsey) said 'If I've missed it I apologise' - that was at half-time," said Pardew.
"It is an awful challenge. The pictures speak for themselves. I thought it was a bad challenge and I was 60 yards from the incident."