B-1 Bomber
The B-1 must get some mention as well, both in terms of “difficulties” and changes from prototype to production. The first 4 B-1A prototypes were nuclear armed penetrators, but production was cancelled. When the program was re-started as the B-1B significant changes in design and re-rolling took place. Changes included dramatically increased all up weight, RCS measures/inlet ramp changes, armament, avionics and changing the crew escape pod to 4 ejection seats.
As for difficulties, there were teething problems with the avionics fits, being derided as “the worlds first self jamming bomber”. A series of fixes took years (if ever) and maintainence hours remain very high.