The result virtually guaranteed the Red Devils a place in the Champions League knockout phase with three games remaining.
But it may come at a price, with Kagawa due for tests on Wednesday to discover the extent of the problem, and Ferguson said: "Kagawa twisted his knee.
"He struggled on for 20 minutes but we will assess in the morning because we don't know the extent of it at the moment."
With goalkeeper Anders Lindegaard also ruled out for a week after suffering a thumb injury in training, Ferguson is likely to be down on numbers for Sunday's crucial Premier League trip to leaders Chelsea.
