It should be noted that the subshells are energy levels as well, called Subsidiary orbital energy levels, so if we sort the subshells in ascending order in terms of their energy levels, it would be s < p < d < f. Orbital Energies The energy of the electron in a hydrogen atom depends...
NBO lists orbitals within each atom according to their energy and their population afterwards. This warning only states that some low energy lying orbitals are less populated than others with higher energy. It cannot be “fixed” since this is a natural consequence of the orthonormalization process ...