Ninety-seven Liverpool fans died almost 33 years ago in a Hillsborough Stadium disaster.
Saturday’s FA Cup semi-final between both Premier League leaders ended in favour of Jurgen Klopp’s side.
Before the game, the English FA had confirmed that a moment of silence would be held before kick-off in tribute to what is seen as the United Kingdom’s worst sporting disaster.
However, the minute’s silence was cut short by referee Michael Oliver after some City fans began chanting and booing.
This very act infuriated Liverpool fans who reacted angrily in the stadium with jeers of their own.
A Manchester City spokesperson said: ‘We are extremely disappointed with the actions of some City supporters during the minute’s silence before today’s game.
“The club sincerely apologises to all those connected with Liverpool Football Club.”
The match ended 3-2 in favour of the Reds who are also chasing the league title and are just one point behind Manchester City.
Jurgen Klopp’s men now await winner of the second semi-final between Chelsea and Crystal Palace to be played on Sunday.