You aren't alone in thinking that there were some questionable calls at the end of last night's Kansas vs Iowa State game. This afternoon the Big 12 conference released a statement acknowledging the fact that their referee's missed a few calls.
The statement from the conference is as follows:
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. 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.
Since referees are considered independenct contractors, the conference can only 'punish' them effectively by not assigning them to future games.