Millwall manager Gary Rowett says an investigation will take place after his side's 2-0 win over Reading at The Den was marred by homophobic chanting.
Referee Keith Stroud stopped play during the first half after being called over by his assistant in front of the East Stand to report an incident emanating from sections of the home support.
Stroud informed both managers what had happened before fans were warned over the speaker system at half-time.
Millwall – who were fined £10,000 last year for racist chanting by their fans – could now be in line for further punishment from the FA.
Rowett said: "I don't necessarily think it was a chant, I think the linesman's heard a comment. There can be lots of comments in a game like that.
"The linesman, with what he's suggested the comment was, has to report it to the referee, who then in turn has to report it to the side of the pitch.
"The club are brilliant at stuff like that, they've worked incredibly hard to make sure things like that don't happen here.
"It's something we don't condone if it has been said. We don't know for sure that it has and they'll investigate, so of course I'll leave it down to them to investigate."
Reading boss Mark Bowen also gave his version of events following the game.
He said: "The referee came over and quietly said he's got to tell us, myself and Gary [Rowett], that there was reported homophobic chants on the far side.
"I don't know if it was to our players or anything. In fairness to our players, they didn't mention it at half-time, we were focused on other things.
"It's sad. From my point of view, as the manager of Reading, it's sad, but it's Millwall's situation to deal with."
On the pitch, Matt Smith and Jon Dadi Bodvarsson netted second-half goals to end Reading's 10-game unbeaten run and leave the Lions outside the Championship play-off places only on goal difference.
Rowett added: "The fans have been brilliant. It's been an absolute pleasure so far this job.
"I'll never criticise the fans for cheering my name but they equally got behind the players and it's the players who were working so hard on the pitch.
"The fans help us here, that's the beauty of it. When the team needs that bit of help, the fans get behind the team and encourage them."
After seeing his side's impressive unbeaten run come to an end, Bowen was frustrated at the Royals' inability to produce their natural game.
He also believed Smith's goal – fired in after Jake Cooper controlled a set-piece in the box but couldn't get a shot away – should have been ruled out.
Bowen said: "On reflection, we forgot to play, really. We knew what was coming, them utilising their strengths with Smith up front and I thought we dealt with the balls coming into the box.
"But we forgot then, when we got possession, to do what we've been good at lately and that's to get the ball down and play. We were sloppy with our passing and never got into a rhythm, so we let ourselves down.
"The disappointing thing is that with the first goal, it staggers me the referee hasn't seen the handball.
"Four of my guys stopped, put their hands up because they've seen it's handball. It was a definite handball in the lead-up."