We have used synchrotron x-ray diffraction to study the low-T homoepitaxial growth on Ag(001) and Cu(001) surfaces. For both systems, we found that a large, temperature-dependent vacancy concentration is incorporated in films grown below 160K. The vacancy trapping occurs concomitantly with substantial changes in the surface morphology, where a non-monotonic temperature dependence of the mean-square surface roughness has been previously observed. For Cu/Cu(001) we also found that the concentration of vacancies incorporated at 110K evolves, upon heating, according to the vacancy annealing behavior well-known from radiation damage studies of bulk copper and it is consistent with the activation energy for vacancy mobility.