Shakespeare said Morgan was fit for the United match, but with fellow defender Robert Huth still recovering after ankle surgery, is hoping new signing Maguire does not face a prolonged spell out.
"Harry hasn't trained fully today as a precaution," the manager told a news conference. "I am hoping there is nothing long term there. It was because of the tackle... and he has had an adverse reaction to it 24 hours later.
"We are taking it easy with Robert, he is sore in the foot and we have to be mindful."
Morgan's absence led Shakespeare to field left back Christian Fuchs in central defence in the cup tie, but the manager said his club captain would be "fighting fit" for the United game.
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"Wes will be involved," he added. "He has trained the last couple of days. Hopefully we won't get an adverse reaction tomorrow but he has trained fully today."
United have made a strong start to the season, taking maximum points from their first two games and scoring eight goals without conceding, while Leicester began with a 4-3 defeat by Arsenal before downing Brighton and Hove Albion 2-0.
With new signings Vicente Iborra (groin) and Kelechi Iheanacho (toe) struggling for fitness, Shakespeare said he was looking forward to the international break after the trip to Old Trafford, where Leicester have not won in the league since 1998.
"Once we get over United we have a couple of weeks and I am hoping we can up (Iborra's) fitness and get him out onto the grass. He hasn't joined in with the squad yet," the manager said.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Christian Radnedge)
