The repeated eruptions of fighting among the Lions supporters left some fans bloodied and younger ones in tears - scenes that will not do anything for the image of the south London club, or the Football Association.
Whelan said 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."
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.
"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."
- Sports & Recreation