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Missiles were thrown at the bus as it arrived for Wednesday's first leg at Anfield, which Liverpool won 3-0.
UEFA said it would investigate the setting off of fireworks, the throwing of objects, acts of damage and crowd disturbances.
"The charges of acts of damage and crowd disturbances relate to incidents involving the Manchester City FC team bus," UEFA said in a statement.
This case will be dealt with by the UEFA Control, Ethics and Disciplinary Body on May 31, it added.