Proximity-induced magnetic effects on the surface Dirac spectra of topological insulators are investigated by scanning tunneling spectroscopic studies of bilayer structures consisting of undoped Bi2Se3 thin films on top of Cr-doped Bi2Se3 layers. For thickness of the top Bi2Se3 layer equal to or smaller than 3 quintuple layers, a spatially inhomogeneous surface spectral gap Δ opens up below a characteristic temperature which is much higher than the bulk Curie temperature determined from the anomalous Hall resistance. The mean value and spatial homogeneity of the gap Δ generally increase with increasing c-axis magnetic field (H) and increasing Cr doping level (x), suggesting that the physical origin of this surface gap is associated with proximity-induced c-axis ferromagnetism. On the other hand, the temperature (T) dependence of Δ is non-monotonic, showing initial increase below which is followed by a 'dip' and then rises again, reaching maximum at T   These phenomena may be attributed to proximity magnetism induced by two types of contributions with different temperature dependences: a three-dimensional contribution from the bulk magnetism that dominates at low T, and a two-dimensional contribution associated with the RKKY interactions mediated by surface Dirac fermions, which dominates at   T <  In addition to the observed proximity magnetism, spatially localized sharp resonant spectra are found along the boundaries of gapped and gapless regions. These spectral resonances are long-lived at H = 0, with their occurrences being most prominent near and becoming suppressed under strong c-axis magnetic fields. We attribute these phenomena to magnetic impurity-induced topological defects in the spin texture of surface Dirac fermions, with the magnetic impurities being isolated Cr impurities distributed near the interface of the bilayer system. The long-term stability of these topologically protected two-level states may find potential applications to quantum information technology.