We report two new first-order Raman modes in the spectra of few-layer MoS$_2$ at 286~cm$^{-1}$ and 471~cm$^{-1}$ for excitation energies above 2.4~eV. These modes appear only in few-layer MoS$_2$; therefore their absence provides an easy and accurate method to identify single-layer MoS$_2$. We show that these modes are related to phonons that are not observed in the single layer due to their symmetry. Each of these phonons leads to several nearly degenerate phonons in few-layer samples. The nearly degenerate phonons in few-layer materials belong to two different symmetry representations, showing opposite behavior under inversion or horizontal reflection. As a result, Raman active phonons exist in few-layer materials that have nearly the same frequency as the symmetry forbidden phonon of the single layer. We provide here a general treatment of this effect for all few-layer two-dimensional crystal structures with an inversion center or a mirror plane parallel to the layers. We show that always nearly degenerate phonon modes of different symmetry must occur and, as a result, similar pseudo-activation effects can be excepted.