Galatasaray had penalty appeals at the start and end of the game turned down, hit the woodwork twice and also forced a magnificent double save out of David de Gea.
"The first 15 minutes we played very well and got the goal," said Ferguson, who saw an early goal from Michael Carrick decide the game.
"At that moment we thought it was going to be a good night.
"But we became very careless and every time we lost the ball, they counter attacked and were a threat.
"Missing the penalty kick kept them in the game."