MLB 2K9, not unlike its most immediate predecessor, has issues. The default calibration between runner and fielder speed is all over the map. Pokey fielder animations turn even simple double plays into uncertainties, but stretching singles into should-be doubles is similarly dicey.
Then again, the computer's A.I. occasionally likes to nap on base and in the field. Even completely misplaying a ball doesn't ensure your opponent will take proper advantage.