United piled on the pressure in the second half but their fate was sealed when Zoltan Gera fired home from close range with just three minutes left.
United's day only worsened there-on-in when Wayne Rooney was sent-off for a second bookable offence when referee Phil Dowd deemed the United striker had deliberately thrown the ball at him.
"The ball was thrown to where the free-kick was being taken," Fergie told MUTV after the 2-0 defeat.
"Did it hit the referee? No!
"But there's no point talking about the referee because we didn't play well enough in the first half and that's why we lost.
"In the first half we never got started.
"They were lively and got stuck in and we respect that because they had lost 4-0 to us a couple of weeks ago.
"It's disappointing we didn't meet the challenge," Fergie added.
"If you lose games in March and April it can cost you.
"Fortunately we have a slender lead at the moment but not a lot and I'm hoping we come back from the internationals back to our best."