The NOvA experiment is an off-axis long-baseline neutrino oscillation experiment measuring $\nu_{\mu}$ disappearance and $\nu_{e}$ appearance in a $\nu_{\mu}$ beam originating at Fermilab. Oscillations are observed in the far detector relative to measurements made in the near detector, with a full simulation of the beam line and detectors being used to perform extrapolation between them. The neutrino simulation uses the GENIE event generator, which contains implementations of numerous theoretical neutrino interaction models applied to a variety of nuclear targets. However, recent data, recent reanalysis of extant data, and continued development of theoretical models have brought to light deficiencies in the default GENIE cross section model, which informs the predicted spectra used to infer oscillation parameters. We explore how uncertainties in this model, together with modifications to GENIE version 2.12.2 based on external information and NOvA Near Detector (ND) data, affect NOvA's oscillation parameter inferences. We also discuss how these uncertainties can be mitigated by judicious analysis design, including usage of the ND data.