We report measurements of phonon dispersions in CaC$_6$ using inelastic X-ray and neutron scattering. We found good overall agreement, particularly in the 50 meV energy region, between the data and the first-principles density-functional-theory calculations. However, on the longitudinal dispersion along the c-axis of the hexagonal representation, we found an unexpected anti-crossing with an additional longitudinal mode, at about 11 meV. At a comparable energy, we observe also unexpected intensity on the in plane direction. This result could help to explain the incorrect interpretation of previous measurements of phonon dispersion in CaC$_6$, which assign a longitudinal character to a transverse mode in the same energy range. By calculating the electron susceptibility from first principles we show that this longitudinal excitation is unlikely to be due to a plasmon and consequently it is probably due to defects or vacancies present in the sample.