The Mountaineers attempted eight fewer free throws in the game, which drew Huggins' ire. The Jayhawks won the conference opener 60-53.
"I can't control what those three blind mice running around out there do," Huggins said on his postgame radio show Saturday.
"What we would all love to see is consistency. Foul there. Foul here. I understand it's a hard job, but they do get paid pretty handsomely for it. Just be consistent."
The Big 12 said Huggins' comments violated its sportsmanship policy. According to the conference, it was Huggins' third time doing so, which carries the fine and a public reprimand.