Interesting that the same thing happened to the Vickers Valiant when it was moved to low altitude roles (and it caused the premature retirement of the type).
In the case of the B-47 the Boeing designers combined the new swept wing technology that George Schairer had found in Germany with thin laminar wings. The thin wings were completely unnecessary and not used in the subsequent B-52 yet they complicated the design, created aeroelasticity problems and structural issues. The Valiant suffered a somewhat short design and development so that it would be ready quickly to carry Britain's nuclear weapons and probably suffered a few minor shortcomings from this. When fatigue did become a problem the Victor and Vulcan were ready.