Mizzou's gripe should be with the Orange Bowl or Sugar Bowl.
Since the Rose Bowl lost #1 OSU to the BCS Title Game, they pick first. They chose Illinois. The #2 pick went to the Sugar Bowl. I assume they chose Georgia. From there, I don't know how they pick them, but the Orange Bowl probably has choice of Kansas or Mizzou, and once they chose Kansas, Mizzou was the odd man due to the 2 team rule.