Rooney was ruled out of the 2-1 victory at Old Trafford because he was still feeling the effects of a heavy collision with an advertising hoarding at the weekend.
The England skipper was hurt in the latter stages of Saturday's 3-0 win over Hull and was limping as the players left the field at the final whistle.
Manager Louis van Gaal had expressed hope the 29-year-old would be fit to face the Potters but has now revealed the problem will be given further examination.
Van Gaal said: "It is his knee but we have to wait for tomorrow to say anything about it because you never know with a knee
My opinion it is not so heavy but I am not a doctor.
"We have to wait for a scan and then we will know more."
United are next in action at third-placed Southampton next Monday night.
Forward Angel di Maria has all but been ruled out of that trip with the hamstring injury that forced him off against Hull, although Van Gaal remains optimistic.
He said: "Di Maria is not so heavy but of course he shall not play against Southampton, I think - but you never know."
Van Gaal also gave an update on another recent injury victim, midfielder Daley Blind, and expressed hope he could be back in action after a knee problem before the end of the month.
He said: "It is not so heavy, but the injury is not next week
Christmas maybe
I think that at the end of December maybe we see light in the tunnel."
Source : PA
Source: PA