Millwall's Championship match against Derby County on Saturday was overshadowed by fans booing players ahead of kick-off for taking the knee.
Since June, games in the Premier League and English Football League have been preceded by the gesture in support of racial equality.
Several high-profile figures, including Micah Richards, have spoken out against the supporters.
Around 2,000 fans were present at The Den for the first time since March.
Millwall went on to lose 1-0, with Jason Knight scoring the only goal of the game for Wayne Rooney's men.
In their post-match press conferences, both Gary Rowett and Rooney condemned the behaviour.
"To hear that is very disappointing and upsetting for a lot of people," the Derby boss said, via BBC Sport.
"I'm pleased with how my team dealt with that. They've had to put that to the back of their minds for the 90 minutes but I'm sure it's something they were thinking about."
Rowett added that his players may no longer make the gesture going forward, saying they "prefer not to take the knee and enact change - do something positively about it".
Ex-Derby forward Colin Kazim-Richards called the incident "an absolute disgrace" on Twitter.
Millwall defender Mahlon Romeo also spoke movingly to the South London Press, saying he was "lost for words".
“Today’s game, to me now, has become irrelevant. The fans have been let back in – which the whole team was looking forward to. But in society there is a problem – and that problem is racism," he said.
“The fans who have been let in today have personally disrespected not just me but the football club... What they’ve done is booed and condemned a peaceful gesture which was put in place to highlight, combat and stop any discriminatory behaviour and racism. That’s it – that’s all that gesture is.
“And the fans have chosen to boo that, which for the life of me I can’t understand. It has offended me and everyone who works for this club – the players and the staff...
“I’m almost lost for words. I don’t know how they thought that would make me feel. I don’t know what they thought taking a knee stood for. But I think I’ve explained it simply enough. I feel really low – probably the lowest I’ve felt in my time at this club."News Now - Sport News