Blues supporters sang 'Anton Ferdinand, you know what you are' in an apparent show of support for John Terry, who faces a police investigation into claims he racially abused the QPR defender during October's west London derby.
However, a Chelsea spokesman said: "It was wholly inappropriate and we don't condone it."
It is unclear whether the Blues could face any action over the chants - but it would not be welcomed by a club whose captain is still fighting to clear his name having denied abusing Ferdinand.
The past nine days have been one of the Blues' most turbulent periods of recent times and Tuesday night's result provided no respite for manager Andre Villas-Boas and his players as they blew a half-time lead and missed a penalty to draw 1-1 at the Cristal Arena.
A win would have seen them put one foot in the last 16 but Group E is now wide open going into the final two rounds of matches, with Chelsea only three points clear of third-placed Valencia.
Villas-Boas said: "We go away and it's a bit tighter, but we have responsibilities that we don't escape. Our job is to qualify first and that's what we'd like to do."
The Portuguese added: "It's not a bad result away from home, but it's a game we expected to win. We have to react."
Chelsea have now won only one of their last four games in all competitions - and even that victory required extra-time.
Villas-Boas said: "When you get a bad run of results, you have to get a win straight away to take you out of the run.
"At the moment, we're trying and chasing hard this win.
"We tried to win, but we collided with good organisation for Genk.
"It's back-to-back games without a win, but there's a draw away from home in the Champions League, we still lead the group, and now we go to Leverkusen."
Genk boss Mario Been was delighted with his side's fightback, especially after their 5-0 thrashing at Stamford Bridge two weeks earlier.
He added: "I know how they talked about us in England.
"Maybe we'll buy the papers and see if they talk about us a little bit better."