Connected CNTs were simulated and the effect of impurities on the frequency of these specific nanostructures was analyzed. For this purpose, the three most likely microscopic imperfections, i.e., doping with Si atoms, vacancy and perturbations to the pure models were simulated. Lastly, the vibrational behavior of imperfect hybrids was evaluated and compared with the behavior of the pure ones. It was pointed out that deficiencies in the structure of hybrids reduces the frequency and as a result, lowers the vibrational stability of the CNTs.