The Japanese midfielder has contributed only two goals and two assists in the Premier League this season and has not completed 90 minutes since the opening-weekend defeat to Everton, having missed two months with a knee injury.
Ferguson is blaming Kagawa's underwhelming first season in English football on the unfamiliar physical style of football.
"The difference between German and English football is that in Germany you can't foul," Ferguson said.
"You are not allowed to touch anyone in Germany, so he [Kagawa] has come from that environment to the Premier League which is totally different.
"There is a physicality to our game which is different from Germany, but next year he'll be better. I thought in the first half-hour [against Real] he was terrific and he was making some great runs through them.
"We thought that was going to be one of our biggest assets in the game, someone to play in the second balls and he was just unlucky with a couple of heavy touches on the ball.
"But he kept on opening them up and if people don't see that, it's actually unfair, but he did really well for us in the first half."
Kagawa is likely to return to the bench for Monday night's FA Cup clash with Reading while Nemanja Vidic, Tom Cleverley, Anderson, Ashley Young and Javier Hernández are likely to play after being overlooked for the Real Madrid clash.