A camera near the locker room where the Alabama players were exiting meanwhile appeared to catch one shout an expletive as he made his way to the field.
Some fans had been stuck outside for an hour during an unusually frigid and wet evening as the area around the stadium locked down for the arrival of the president's motorcade.
Trump, who has made respectful observation of the national anthem at sporting events a fiercely divisive political issue, stood at midfield and sang some of the "Star-Spangled Banner," while remaining silent at other times.
The mixed reception could be a worry for the White House, coming deep in Trump country in a contest watched by fans from two nominally Republican states.
But the president's eldest son Donald Trump Jr denied there had been any jeering. "Sounds like some serious cheering to me," he wrote while retweeting a video clip of the incident.
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