Cyclones fans were incensed when the referees missed a potential charging violation against the Jayhawks' Elijah Johnson in the closing seconds of regulation time.
The officials then called a foul on Iowa State's Georges Niang as he and Johnson battled for the ball.
Johnson sank a pair of score-tying free throws, forcing an overtime, during which the Jayhawks went on to win 108-96.
"The Big 12 Conference acknowledges that officiating errors were made at the end of regulation during last night's Kansas at Iowa State men's basketball game," league officials said in a statement issued Tuesday.
"The plays have been reviewed and appropriate measures will be taken by the Coordinator of Men's Basketball Officials to adjust the number of future assignments for the two officials involved in conjunction with Conference policies."