City, who won the game 4-1, said an object was thrown towards the bus in a residential area.
Greater Manchester Police said they had launched an investigation after reports of criminal damage and said there were no injuries, adding that the bus continued with its journey.
"Incidents of this kind are totally unacceptable, and we strongly condemn the actions of the individual(s) responsible," City, the reigning Premier League champions, said in a statement.
"We will fully support Greater Manchester Police's investigation into this incident in any way we can."
City also said the club were disappointed to have heard "inappropriate chants" from their fans during the game.
"We regret any offence these chants may have caused and will continue to work with supporter groups and officials from both clubs to eradicate hateful chanting from this fixture," the statement added.
