The Dutchman is struggling to overcome a knee meniscus injury, which has kept him out all campaign.
Malacia, who is now 24, was signed by manager Erik ten Hag during his first summer in charge.
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The Athletic report that Malacia did not listen to United regarding his injury in the summer.
He was told to have the surgery in London with a United-picked surgeon, but he chose someone else in the Netherlands.
United accepted his request, but the operation did not go as had been planned.
Malacia worked his way to fitness in the fall, but cartilage fragments were noticed in later scans, and he had a second surgery.