N-body simulations make unambiguous predictions for the abundance of substructures within dark matter halos. However, the inclusion of baryons in the simulations changes the picture because processes associated with the presence of a large galaxy in the halo can destroy subhalos and substantially alter the mass function and velocity distribution of subhalos. We compare the effect of galaxy formation on subhalo populations in two state-of-the-art sets of hydrodynamical CDM simulations of Milky Way mass halos, APOSTLE and AURIGA. We introduce a new method for tracking the orbits of subhalos between simulation snapshots that gives accurate results down to a few kiloparsecs from the centre of the halo. Relative to a dark matter-only simulation, the abundance of subhalos in APOSTLE is reduced by 50% near the centre and by 10% within r200. In AURIGA the corresponding numbers are 80% and 40%. The velocity distributions of subhalos are also affected by the presence of the galaxy, much more so in AURIGA than in APOSTLE . The differences on subhalo properties in the two simulations can be traced back to the mass of the central galaxies, which in AURIGA are typically twice as massive as those in APOSTLE . We show that some of the results from previous studies are inaccurate due to systematic errors in the modelling of subhalo orbits near the centre of halos.