Heteroepitaxial YBa2Cu3O7-delta thin films have been deposited onto nominal (001)MgO substrates by pulsed laser deposition. For some of these films, Rutherford backscattering spectrometry analysis revealed anomalous variations in the backscattered yield at the substrate level during [001] YBa2Cu3O7-delta axial channelling. A novel angular-dependent ion channelling technique has been developed to investigate these effects. It has been shown that the anomalies arise from an epitaxial misorientation between the lattices of the substrate and deposit. Strong correlations were found between the magnitudes of the misorientations, the densities of spiral features on the deposit surface and the critical current densities exhibited by the deposits. It is proposed that the misorientation arises due to vicinal offcut of the substrate surface, which leads to a lower density of threading dislocations and hence less flux pinning.