In Kohn-Sham density functional theory (KS DFT) a fictitious system of noninteracting particles is constructed having the same ground-state (GS) density as the physical system of interest. A fundamental open question in DFT concerns the ability of an exact KS calculation to spot and characterize the GS degeneracies in the physical system. In this Letter we provide theoretical evidence suggesting that the GS density, as a function of position on a 2D manifold of parameters affecting the external potential, is "topologically scarred" in a distinct way by degeneracies. These scars are sufficiently detailed to enable determination of the positions of degeneracies and even the associated Berry phases. We conclude that an exact KS calculation can spot and characterize the degeneracies of the physical system.