We report a size-inconsistency problem for several functionals within reduced density matrix functional theory. Being explicit functionals of the natural orbitals and occupation numbers, instead of the one-body reduced density matrix, many of the approximate functionals are not invariant under unitary transformations in the subspace of degenerate occupation numbers. One such transformation mixes the degenerate natural orbitals of identical independent subsystems, delocalizing them. Noninvariance under this transformation results in size inconsistency for some of the approximations while others avoid this pathology by favoring orbital localization.