Manager Manuel Pellegrini says Manchester City's supporters have the right to boo the Champions League anthem in protest at Uefa.
The club were reported after fans were heard jeering the music before their 2-1 home win over Sevilla.
"I think everyone has the right to boo or protest on different things," the Chilean told a news conference ahead of Tuesday's return game in Spain.
"If they boo then they feel there's something Uefa is not doing right."
On Sunday, City captain Vincent Kompany said it was "a joke" that Uefa is investigating the club.
"There is nothing holy about the Champions League anthem," said the Belgium defender.
"We have played many games in Europe where there has been racial abuse - we have had to put up with it."
City supporters are understood to have regularly booed the Champions League anthem over the past year.
It is not the first time Manchester City supporters have voiced their anger against Uefa.
Last year a City fan group led a protest against European football's governing body after 650 CSKA Moscow supporters gained access to the Khimki Arena for their Champions League game, despite the Russian club being ordered to play it behind closed doors.
The case against Manchester City will be considered at a meeting of Uefa's disciplinary body on 19 November and a charge could follow.