The weapons bay...
It was arranged like internal box magazines, to put it bluntly. The missiles were stacked in rows, and fed to the launch position.
They couldn't get it to stop consistantly jamming, which could be deadly if there were real warheads (hangfire city).
Also, there was also a political decision. Lockheed Martin's F-117 was delivered on time and complete, while the B-2 development was protracted and over-budget, so they rewareded Lockheed Martin by adopting the F-22 over the YF-23.