Fights broke out in the second half of the game with several in attendance left with bloodied faces and cameras picking up one supporter appearing to be in possession of a police hat.
Early reports suggested the main confrontation was between fellow Millwall fans, which resulted in further altercations with police stepping in to try and calm matters down.
Millwall boss Kenny Jackett was not aware of the scuffles when quizzed soon after the full-time whistle.
"I've just heard about that," he said. "I wasn't aware of any fighting during the game, not aware of any problems. I'll need to examine the facts before I can give an opinion.
"I promise you, I wasn't aware of it during the game. I am not saying it didn't happen. Until I see it, it is difficult to form an opinion.
"We want to be talking about football. I need to be able to form my own opinion. I am sure the evidence is there. I am not denying that."
Jackett vowed the club were doing all they could to rid themselves of their reputation for hooliganism.
"That has been our greatest challenge," he said. "We want to try and work hard to keep momentum going forward. I understand what you are saying. If there was crowd trouble... It will hold us back if that happens repeatedly.
"We have worked very hard, the chief executive and chairman, to do everything we possibly can to be trouble-free. We have had high-profile games that have gone very well. We have done everything we possibly can."
After being told some children were carried out crying, he said: "I am very sorry if that is the case. Until I see those images, for me to comment is a tough one."
Both the FA and Millwall have condemned the actions of those involved and Wigan chairman Dave Whelan admitted he was bewildered by the incidents.
"I can't understand why the Millwall fans would fight each other," he said.
"I understand if they want to fall out with the visiting team, but why would they fall out amongst themselves? It just gives football a very, very poor reputation.
"We know Millwall are a tough club, their team's tough to play, the supporters are Millwall Millwall Millwall... straight through. But don't fight each other. I couldn't understand that."
Latics manager Roberto Martinez spoke of his disappointment on hearing of the violence, although - like Jackett - he was unaware of it during the match.
"I didn't (see it)," the Spaniard said on ESPN. "People are mentioning now there were some incidents and that's disappointing.
"The game on the pitch was exciting and there was always something to be concentrating on so it's disappointing when that happens."