Mancini had hoped United would progress at the expense of Real Madrid this week to provide a distraction from their increasingly strong Barclays Premier League title march.
He said: "It is clear now it is worse for us because they can put all their strength in the championship.
"It was better they stayed in the Champions League. When you play an important game every three days it is more difficult.
"But it was difficult (for us) before the game against Madrid.
"I think they have an advantage because 12 points are too much but our job is to try until the end of the season."