The formation and propagation of ion phase-space vortices are observed in a numerical particle-in-cell simulation in two spatial dimensions and with three velocity components. The code allows for an externally applied magnetic field. The electrons are assumed to be isothermally Boltzmann-distributed at all times, implying that Poisson's equation becomes nonlinear for the present problem. Ion phase-space vortices are formed by the nonlinear saturation of the ion-ion two-stream instability, excited by injecting an ion beam at the plasma boundary. We consider the effect of a finite beam diameter and a magnetic field, in particular. A vortex instability is observed, appearing as a transverse modulation, which slowly increases with time and ultimately breaks up the vortex. When many vortices are present at the same time, we find that it is their interaction that eventually leads to a gradual filling-up of the phase-space structures. The ion phase-space vortices have a finite lifetime, which is noticeably shorter than that found in one-dimensional simulations. An externally imposed magnetic field can increase this lifetime considerably. For high injected beam velocities in magnetized plasmas, we observe the excitation of electrostatic ion-cyclotron instabilities, but see no associated formation of ion phase-space vortices. The results are relevant, for instance, for the interpretation of observations by instrumented spacecraft in the Earth's ionosphere and magnetosphere.