I assume you have used a pseudopotential with 2 electrons in the core, such as the default PseudoDojo. In that case, they are not counted in the analysis.
In a Mulliken Population analysis, the electron density is projected onto the basis functions, so if you have used the PseudoDojo-Medium basis set, there are two 2s-like orbitals, two 2p-like orbitals and one 3d-like orbital. Note that the populations are quite small on the second and fourth basis functions, as they are not the primary basis functions for describing that orbital.
