“We told the N.C.A.A. what we’d like to have,” Pauga said. “It doesn’t always work. Remember, not only do they have to get all of us there, but 16 teams lose on Thursday, and 16 teams lose on Friday, and they don’t know who they are and where they’re going.”

The same planes ferry women’s teams for opening-round games Saturday and Sunday. So on Thursday, the N.C.A.A. had to get 32 women’s teams to their destinations and retrieve 16 men’s teams that lost that day — without knowing which teams would lose and where they needed to go. The same happened Friday.

Harvard had requested that its traveling party of 93 be taken home Thursday night if the Crimson lost, the associate athletic director Nathan Fry said. The afternoon before the game, Harvard was told it would not be able to travel until Friday morning. But then Harvard defeated Cincinnati, which went home Friday morning instead.

That same plane had carried New Mexico State home hours before, part of a dizzying week for the charter.

On Tuesday, it took Wisconsin-Milwaukee to Buffalo, and then flew south to take Pittsburgh to Orlando, Fla. On Wednesday, the plane went to Atlanta to pick up Mercer and take it to Raleigh, N.C. It then picked up North Carolina’s team and flew to San Antonio. On Thursday, the plane headed to Shreveport, La., to take the Northwestern State women’s team to Knoxville, Tenn., and then hopped over to Nashville to take the Middle Tennessee State women’s team to Seattle. Then it headed to Spokane to grab the loser of the San Diego State-New Mexico State game.

The system does not allow much flexibility. On Thursday afternoon, San Diego State and New Mexico State were informed that the loser of their game that night would travel home after the game, at 12:30 a.m. But when the game started late and then went to overtime, university officials asked to stay overnight.

They were told that was not possible, which prompted Fisher’s indictment. The New Mexico State associate athletic director Steve Macy took to Twitter to complain in real time.