Mancini's policy of travelling straight home following European games backfired after Thursday's defeat at Dynamo Kiev as City's flight did not land in Manchester until 5am on Friday.
The delay is believed to have been caused by issues over a gas bottle in City's medical kit and it meant the players barely slept just two days before Sunday's FA Cup quarter-final against Reading.
Mancini stood by his policy, saying: "If we left on Friday, we would have lost another day. Usually after a game the players don't sleep so we felt it was better to get them back and try to get them right for Sunday.
"This is one of the problems we have playing every three days. We are playing on Sunday at 5pm and I hope we can recover in time."
Midfielder Nigel De Jong backed his manager's decision, saying: "I don't think it will affect us. We're not little kids any more. We've all got experience of how to handle this schedule and make sure we are right and ready for them on Sunday. I'm sure I'll be okay."