Duke's Miles Plumlee was called for a flagrant foul late in the second half when he was deemed to have thrown an elbow on a rebound.
Clemson's Tanner Smith, who was involved in the play, said Plumlee didn't catch him with an elbow.
"I told the ref I didn't get hit," Smith said. "My face is fine. But I don't know what the rule is. They have different rules for flagrant fouls."
Clemson coach Brad Brownell wasn't playing the moral victory card after the Tigers' narrow loss. It dropped Clemson to 1-2 in the league with a trip to Miami on Wednesday.
"We're here to win games," Brownell said. "I understand that Duke's a terrific team and all of that but we had opportunities to win the game. We're not having a good year at all so everybody can say we had a good effort or that it was a good try. You can't let that fool you ... We didn't get it done."
Maybe the Tigers need to try something different against Duke. In their last four meetings, the Tigers have shot just 20 percent from 3-point range against Duke.
Freshman guard Austin Rivers had a season-low four points, attempting a season-low seven shots. He didn't get his first basket until 10 minutes, 14 seconds remained in the game.