We use density functional calculations to investigate the accommodation and migration of oxygen vacancies in bulk hexagonal YMnO3, and to study interactions between neutral ferroelectric domain walls and oxygen vacancies. Our calculations show that oxygen vacancies in bulk YMnO3 are more stable in the Mn-O layers than in the Y-O layers. Migration barriers of the planar oxygen vacancies are high compared to oxygen vacancies in perovskites, and to previously reported values for oxygen interstitials in h-YMnO3. The calculated polarization decreases linearly with vacancy concentration, while the out-of-plane lattice parameter expands in agreement with previous experiments. In contrast with ferroelectric perovskites, oxygen vacancies are found to be more stable in bulk than at domain walls. The tendency of oxygen vacancies to segregate away from neutral domain walls is explained by unfavorable Y-O bond lengths caused by the local strain field at the domain walls. arXiv:1807.01509v1 [cond-mat.mtrl-sci]