The 30-year-old US superstar came straight from hard training into the tuneup meet for the Olympic trials in Omaha this month.
He finished fourth in the 200m freestyle won by Townley Haas in 1min 47.86sec, with Phelps, clocking 1min 48.73.
The setback came a day after Phelps won the 100m free and finished second to Singapore's Joseph Schooling in the 100m butterfly.
The meeting is one of three elite events this weekend where US swimmers are warming up for the demands of trials, and overseas competitors are prepping for the Rio Games themselves.
In other Austin action, American Chase Kalisz posted the third-fastest time in the world this year in the 400m individual medley, winning in 4:11.51.
