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