We describe the occurrence of computational artifacts when the principal layer method is used in combination with the cluster approximation for the calculation of electronic transport properties of nanostructures. For a one-dimensional gold chain, we observe an unphysical band in the band structure. The artificial band persists for large principal layers and for large buffer sizes. We demonstrate that the assumption of equality between Hamiltonian elements of neighboring layers is no longer valid and that a discontinuity is introduced in the potential at the layer transition. The effect depends on the basis set. When periodic boundary conditions are imposed and the k-space sampling is converged, the discontinuity disappears and the principal layer method can be correctly applied by using a linear combination of atomic orbitals as basis set.