Born cross sections for the processes $e^+e^- to omegaeta$ and $e^+e^- to omegapi^{0}$ have been determined for center-of-mass energies between 2.00 and 3.08 GeV with the BESIII detector at the BEPCII collider. The results obtained in this work are consistent with previous measurements but with improved precision. Two resonant structures are observed. In the $e^{+}e^{-} to omegaeta$ cross sections, a resonance with a mass of $(2179 pm 21 pm 3)text{MeV}/c^2$ and a width of $(89 pm 28 pm 5)text{MeV}$ is observed with a significance of 6.1$sigma$. Its properties are consistent with the $phi(2170)$. In the $e^{+}e^{-} toomegapi^{0}$ cross sections, a resonance denoted $Y(2040)$ is observed with a significance of more than 10$sigma$. Its mass and width are determined to be $(2034 pm 13 pm 9)text{MeV}/c^2$ and $(234 pm 30 pm 25)text{MeV}$, respectively, where the first uncertainties are statistical and the second ones are systematic.