In this article, we introduce a general theoretical framework to analyze non-consistent approximations of the discrete eigenmodes of a self-adjoint operator. We focus in particular on the discrete eigenvalues laying in spectral gaps. We first provide a priori error estimates on the eigenvalues and eigenvectors in the absence of spectral pollution. We then show that the supercell method for perturbed periodic Schrödinger operators falls into the scope of our study. We prove that this method is spectral pollution free, and we derive optimal convergence rates for the planewave discretization method, taking numerical integration errors into account. Some numerical illustrations are provided.