In this paper we consider the Universe at the late stage of its evolution and deep inside the cell of uniformity. At these scales, the Universe is filled with inhomogeneously distributed discrete structures (galaxies, groups and clusters of galaxies). Supposing that a small fraction of colored objects escaped hadronization and survived up to now in the form of quark-gluon nuggets (QNs), and also taking into account radiation, we investigate scalar perturbations of the FRW metrics due to inhomogeneities of dustlike matter as well as fluctuations of QNs and radiation. In particular, we demonstrate that the nonrelativistic gravitational potential is defined by the distribution of inhomogeneities/fluctuations of both dustlike matter and QNs. Consequently, QNs can be distributed around the baryonic inhomogeneities (e.g., galaxies) in such a way that it can solve the problem of the flatness of the rotation curves. We also show that the fluctuations of radiation are caused by both the inhomogeneities in the form of galaxies and the fluctuations of quark-gluon nuggets. Therefore, if QNs exist, the CMB anisotropy should contain also the contributions from QNs. Additionally, the spatial distribution of the radiation fluctuations is defined by the gravitational potential. All these results look physically reasonable.