Too many 300 plus teams is the sole answer here. Losing to Omaha was really bad, but look around, every year a lot of teams have a surprise loss like that. To me the biggest flaw in the RPI is the absence of margin of victory being a component. You can break every NCAA scoring record and crush the #309 team by a million, and it carries as much weight if you escaped a monumental upset and won on a last second basket...
Minnesota is a prime example of how to do it. They feasted on the 100 level teams. They didn't blow anyone out, played a couple pretty close, and the only top 25 team they played was Florida State and lost. They're 11-6 in Big Ten play and beat similar teams as Iowa. Yet nowhere close in the RPI.