Police were forced to intervene after bloody fighting broke out amongst a section of the London club's support
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 their 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.
The violence should be attributed to 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."