We live in an F-35 world where the small opening to allow the gun to fire can upset the aircraft enough for the gun to miss and the gun installation was part of the A design from the beginning.
Aaargh, Sorry, but that fits firmly in the That's Why You Have Wind Tunnels And CFD bracket. So let me take a wild guess and suggest that the problem was obvious from day one, or at least from the point where the big 5-barrel 25-mm was substituted for the ATK-Rheinmetall 27, but some smartar*e waved it away by a PowerPoint concluding "addressable via flight control software", and a more senior schedule-driven person (preoccupied no doubt by the jet's unexpected acquisition of 3000 pounds of ugly surplus fat) declared said PPT to be the truth.
Not that it matters too much, as a gun on a stealthy bomber is about as relevant as pikes and boarding ladders on a submarine.