The 27-year-old was visibly uncomfortable while the squad did a number of short sprints during a training session.
Alex Ferguson has previously said that Rooney needs up to three games to get match-fit after an injury break and will be desperate to keep the forward fit after he missed most of December and January through injury.
With United still fighting on three fronts, Ferguson will want to get Rooney up to match speed as soon as possible to supplement the goals of strike partner Robin van Persie, especially for next month's Champions League showdown with Cristiano Ronaldo's Real Madrid.
There are also increasing concerns over the well-being of Ashley Young who left Old Trafford after United's 2-1 victory over Liverpool on crutches.
It had been hoped that Young would only be sidelined for a maximum of two weeks but is more likely to return at some stage next month after the initial prognosis fell well short of the mark.
Meanwhile, former United skipper Gary Neville has rejected claims he was asked to "nail" David de Gea following Manchester United's Premier League draw with Tottenham on Sunday.
Neville, a Sky Sports analyst, was typically forthright in his assessment of De Gea's weak punch, which led to Clint Dempsey's injury-time equaliser and indicated Alex Ferguson would share the same displeasure so obvious in the body language of his players.
Even though others disagreed, the assessment seemed pretty astute given Neville's knowledge of United, and the high praise he has earned in his role as a TV pundit.
However, it was subsequently suggested by former Sky Sports presenter Richard Keys that Neville had been asked to highlight De Gea's flaws, although he did not say who by.
Keys said of Neville this morning: "I think he was sent out with an agenda. I don't think Gary would have done that had he not been told: 'Listen, finger him'.
"I don't think you can nail a goalkeeper in that way can you?"
When informed of this observation via Twitter this morning, Neville's response was straight to the point.
"This is not interesting it's wrong," he said.
"I never have and never will take instructions off anybody to say anything!"
Neville subsequently removed the Tweet, even though the response was understandable given no one has questioned his objectivity before.
In addition, the England assistant-coach had already underlined how highly he rates De Gea in another Twitter posting.
"For the record I think De Gea can be a great GK. He is young in an unforgiving environment and will physically mature in next 2 years."
It has been suggested Real Madrid would like to sign the 22-year-old, who has started 10 of United's last 11 games.
And Ferguson has been linked with numerous potential replacements, including Stoke's Asmir Begovic, having seemed to lose faith with De Gea's deputy, Anders Lindegaard, following his error-strewn performance at Reading at the beginning of December.
Nevertheless, it does seem likely De Gea will remain United's first choice at least until the end of the season, and England's World Cup-winning keeper Gordon Banks is amongst those who think Neville went too far.
"I was very upset to hear Gary Neville talking about how the players were disgusted with him (De Gea), how they were looking at him, after he hadn't punched the ball quite clear enough," said Banks.
"I thought to myself, 'hang on a minute, it's not just the goalkeeper that makes mistakes, everybody makes mistakes in football matches'.
"I couldn't quite believe that, because if anything he would've liked a bit of a lift.
"I found that a bit strange that he (Neville) was saying they'd go back in the dressing room and give him a telling off."
United are expected to reach some kind of agreement over Wilfried Zaha's move from Crystal Palace before the transfer window shuts next week.
The Red Devils were hoping to come to an arrangement similar to the one they reached with Fulham two years ago, when they agreed to buy Chris Smalling but left him to end the season at Craven Cottage before completing the transfer.
However, the Football League believe the only way for Zaha to remain at Palace and become a United player would be for the Premier League title contenders to buy him outright, then loan him back.