The pity is that such mindless aggression from a minority must even be mentioned. The positive is that, for the vast majority of the game, Wigan played enough fine football to ensure their excellent achievement warrants the attention.
There was only a brief period in this game, for about 15 to 20 minutes in the second half, that the win looked any way in doubt.
Even that, though, ended with Roberto Martinez's side only illustrating their clear superiority over the Championship side.
With Wigan just about standing up to Millwall's aerial attacking, the ball came out to Arouna Kone. Not for the first time, he alleviated the pressure with a smart turn few players on the pitch could have replicated. The ball was worked up the pitch with speed, through James McCarthy, and eventually to the dominant Jordi Gomez. With a wondrously weighted pass, he picked out Callum McManaman and the man of the match picked Millwall off.
And, without doubt, the final is set to go down as one of the highest peaks in Wigan's 81-year history.
The club's owner, Dave Whelan, was understandably very emotional. He had his career ended by a tackle in the 1960 FA Cup final in Blackburn Rovers' 3-0 defeat to Coventry. Manager Roberto Martinez has called for him to lead out the team at Wembley for the showpiece.
"We were together for at least five minutes," the Spaniard explained afterwards. "All he said was 'we've done it'. He's an example of a human being that just sets incredible targets, sometimes unthinkable. He had a dream 15 years ago, when we were at the bottom of the lowest professional league, and now we have an FA Cup final."
From that high, we have the low of events in the Millwall end. One of the starkest things that can be said was that this was only one of the worst moments in the club's history. Unfortunately, they have a history that has now only been highlighted on one of the grandest stages.
Although manager Kenny Jackett tactically explained he didn't want to say too much until he had seen the footage, it was difficult not to feel some sympathy. It genuinely appeared as if he had been too concentrated on the game to notice the chaos going on to his right. He could have offered a lot more condemnation, however.
In separate periods of the second half and in separate sections of the Millwall end, there were groups of up to 20 fans attacking each other with some ferocity.
"It's not [part of our game] and never has been," Jackett said. "We want to be talking about the football, and so do I. It's not something I can sum up right now. I need some time to be able to form my own opinions.
"That's been our greatest challenge. We're working on attendances of 9,000, 10,000 average, in a very competitive championship. To some degree, that's our greatest challenge. If crowd trouble is going to be continually brought up with Millwall, that will hold us back. I'm very sorry if that is the case."
There was a certain irony in the fact that the trouble came around the time of the club's most promising part of the game.
For a good 20 minutes, Millwall had Wigan under real pressure. A set-piece was fired just over, Antolin Alcaraz almost deflected one cross into his own net.
One of the reasons that an under-resourced Wigan side have been able to regularly stay up and reach occasions such as this, though, has been their resilience. They are not usually intimidated in any form, not by tenacity or talent. Indeed, as Sean St Ledger was booked for a brutal foul on McManaman, the Wigan midfielder's own offence against Newcastle United was brought to mind. Generally, even if it leads to the occasional thrashing against superior sides, they try to play every match on their own terms.
That was certainly the case in the first half here. Not only did they assuredly control the game, they made it count.
With one supreme 26th-minute run, Kone lifted the ball over Mark Beevers' head and sent over a fine cross for Shaun Maloney. The forward expertly guided the ball past the goalkeeper.
It set the tone, and set up a fine win for Wigan.
Unfortunately, that is not all everyone will remember about the day. The trouble, however, has moved well beyond the football.