United were trailing to Yaya Toure's 53rd minute goal when Scholes, famed for his poor tackling technique, and Pablo Zabaleta went in with their feet high for a bouncing ball.
The City defender just about connected with the ball while Scholes' studs ripped a gash in Zabaleta's thigh and earned a straight red card after 72 minutes.
"With Paul we've seen it over his career. He's had unbelievable moments and is a great player, one of the greatest ever at our club," Ferguson said of the 36-year-old former England man who could be in his last season at Old Trafford.
"But he has these red mist moments and this was another one. He was a bit unfortunate, maybe, as he went for the ball and it bounced up and he's gone through and caught the boy on the thigh."
Ferguson, however, did not blame his team's defeat on the sending off and instead pointed to poor defending in the lead-up to the goal and two early misses by striker Dimitar Berbatov.
"The red card didn't kill the game, I thought we played better after it," he said. "The first 15 minutes after halftime cost us the game - slack moments - Edwin (van der Sar) had a bad kick out and Michael Carrick couldn't hold it and it was a goal.
"From then on, they were defending apart from a couple of counter-attacks. It's disappointing as we should've been ahead in the first half as we were the better team.
"The chances that Dimitar missed - there was a great save by the goalkeeper but the second chance, from under the bar, if he'd have scored there, I had a feeling whoever scored first would win the match."
The defeat ended Ferguson's hopes of matching his 1999 treble but United are still in the hunt for the Champions League, where they face Schalke 04 in the semi-finals, and the Premier League.
"We're getting recovered to get ready for the game on Tuesday. "You've got to recover and get on a winning streak again and it's a major game up at Newcastle."
