Competition between the two swimmers goes back to the 2012 London Olympics, where le Clos beat out Phelps in the race, earning the gold medal while Phelps placed second.
But Phelps said he didn't mean to aim any resentment toward le Clos Monday.
"I just had music going on in my head. I had thoughts going on in my head, spitting water a little bit all over the place, so I was in my own zone," he told the "Today" show on Tuesday. "I was not intentionally mean mugging him or giving him a dirty look."
After the angry face, Phelps qualified, coming in second place behind Tamas Kenderesi, of Hungary. Le Clos qualified in fourth.
Phelps went on to win gold in the 200m fly Tuesday night, earning his 20th gold medal of his career. He has a total of 24 Olymipic medals.