The former Wales international picked up the injury in the first leg of the last 16 encounter in France and is struggling to be fit for the Old Trafford return with the tie evenly poised at 1-1.
Ferguson confirmed: "The one doubt is Ryan Giggs. The blow he took in the Lyon away game has proved a bit more complicated than we first thought.
"It's held him back from training as much as we'd like. He did a bit on Monday morning, and on Saturday morning - he had Sunday off for treatment - so he is a doubt."