Police were forced to intervene after bloody fighting broke out amongst a section of the London club's support, overshadowing Wigan's victory and progression to the final
The trouble had been brewing for much of the second half but intensified shortly after Latics attacker Callum McManaman handed Roberto Martinez’s side a two-goal lead with barely 10 minutes remaining in the match.
A small cluster of Millwall fans, a club notorious for its hooligan firms, began fighting between themselves, but the conflict quickly spread across the Millwall section of the stadium.
There were fists flying and bloodied faces in the crowd, with a general air of panic amongst the innocent bystanders trying to avoid the violence.
Police attempted to intervene and were met with vicious resistance, with riot helmets flung through the air - and the MET police have since confirmed that 10 arrests have been made.
The violence should be attributed to a small minority of fans, with many Millwall supporters escaping the fighting before applauding their defeated side’s efforts at the end of the match.
But the scenes, the most bloodied in the short history of the new Wembley stadium, will sour an otherwise engaging and fairly contested on-field match which saw Wigan progress to the final of the FA Cup.
Afterwards Millwall manager Kenny Jackett told ESPN: "I didn't see or hear anything at all. It's the first I've heard of it and I didn't see anything. Nothing has been brought to my attention.
"I've come out straight after the game with the disappointment of a loss. I'd need all of the facts and need some time before I form an opinion."
Meanwhile, Wigan chairman Dave Whelan expressed his bewilderment, saying on BBC Radio Five: "I can't understand why the Millwall fans would fight each other.
"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."