The England striker scored the game's only goal from a free-kick, before going down holding his knee in the 76th minute and he had to be replaced by Anthony Martial.
United return to Premier League action on Saturday when they travel to Huddersfield and Mourinho is not sure if Rashford will be available, but he does expect Phil Jones to return to the starting eleven.
"With Rashford, I thought it was cramp because he was running so much - I thought it was muscular fatigue," Mourinho said.
"But no, he told me he felt something in his knee. It didn't look to me like a big thing but we don't know.
"Phil Jones was on the bench because he felt that if we really needed him, he could [play]. So if he was at that stage today, on Saturday I think he will be in a condition to play. For Eric Bailly, I think it will be difficult.
"Hopefully some of them [can return at Huddersfield] but I don't know. I don't know about Paul, I don't know about Fellaini."