We study the non-perturbative superpotential in E_8 x E_8 heterotic stringtheory on a non-simply connected Calabi-Yau manifold X, as well as on itssimply connected covering space \tilde{X}. The superpotential is induced by thestring wrapping holomorphic, isolated, genus 0 curves. According to the residuetheorem of Beasley and Witten, the non-perturbative superpotential must vanishin a large class of heterotic vacua because the contributions from curves inthe same homology class cancel each other. We point out, however, that incertain cases the curves treated in the residue theorem as lying in the samehomology class, can actually have different area with respect to the physicalKahler form and can be in different homology classes. In these cases, theresidue theorem is not directly applicable and the structure of thesuperpotential is more subtle. We show, in a specific example, that thesuperpotential is non-zero both on \tilde{X} and on X. On the non-simplyconnected manifold X, we explicitly compute the leading contribution to thesuperpotential from all holomorphic, isolated, genus 0 curves with minimalarea. The reason for the non-vanishing of the superpotental on X is that thesecond homology class contains a finite part called discrete torsion. As aresult, the curves with the same area are distributed among different torsionclasses and, hence, do not cancel each other.