We consider model order reduction based on proper orthogonal decomposition (POD) for unsteady incompressible Navier-Stokes problems, assuming that the snapshots are given by spatially adapted finite element solutions. We propose two approaches of deriving stable POD-Galerkin reduced-order models for this context. In the first approach, the pressure term and the continuity equation are eliminated by imposing a weak incompressibility constraint with respect to a pressure reference space. In the second approach, we derive an inf-sup stable velocity-pressure reduced-order model by enriching the velocity reduced space with supremizers computed on a velocity reference space. For problems with inhomogeneous Dirichlet conditions, we show how suitable lifting functions can be obtained from standard adaptive finite element computations. We provide a numerical comparison of the considered methods for a regularized lid-driven cavity problem.