Jones suffered a suspected fractured cheek after being caught by the elbow of Clint Dempsey, while Young was forced off due to Dickson Etuhu's tackle in what Sir Alex thought was a "very aggressive" second half.
"It was an elbow from Dempsey but I don't think it was intentional," Sir Alex told reporters after the match.
"He caught Jones and we'll send him for an x-ray. We'll see on Thursday but it doesn't look great.
"But there were some very aggressive tackles in the second half and Ashley Young paid the price of that. He was hurt and had to come off as well and will be out for two or three weeks.
"We are picking up injuries at the moment. Rio [Ferdinand] got a knock on the foot on Sunday at QPR but he should be available for the Blackburn game."That would rule Ferdinand out of United's Boxing Day encounter against Wigan Athletic, with Nemanja Vidic also unavailable long-term with a knee injury.