Abstract Nuclear power reactors are the most intense man-made source of antineutrino's and have long been recognized as promising sources for coherent elastic neutrino-nucleus scattering (CE$\nu$NS) studies. Its observation and the spectral shape of the associated recoil spectrum is sensitive to a variety of exotic new physics scenarios and many experimental efforts are underway. Within the context of the reactor antineutrino anomaly, which initially indicated eV-scale sterile neutrino's, the modeling of the reactor antineutrino spectrum has seen a significant evolution in the last decade. Even so, uncertainties remain due to a variety of nuclear structure effects, incomplete information in nuclear databases and fission dynamics complexities. Here, we investigate the effects of these uncertainties on one's ability to accurately distinguish new physics signals. For the scenarios discussed here, we find that reactor spectral uncertainties are similar in magnitude to the projected sensitivities pointing towards a need for $\beta$ spectroscopy measurements below the inverse $\beta$ decay threshold.