If a flawed mathematical paper were used as the basis for what then became a flawed cryptography algorithm, I can see that having impact if the bad guys noticed the flaw first. But yes, I expect examples like that would be comparatively rare.
In cryptography the math is almost always the strongest part, and it is the side-channel attacks and implementation mistakes that let the bad guys in. When it is the math, the flaw is often that the algorithm has all the desirable properties proved in a number of papers, but has some exploitable structure that analysts can turn into an attack.
