One of the challenges of modern crystallography of complex systems (complex metallic alloys, proteins, aperiodic crystals and quasicrystals) is to properly describe the disorder in these systems and discuss correctly the refinement results in terms of the structural disorder. In this paper we briefly discuss a new approach to phasons and phonons in quasicrystals and focus on the new theory of phonons in these materials. A newly derived correction factor for phonons in the form of the Bessel function is the approximated way of describing optic modes in the phonon spectra of quasicrystals. It is applied to a real decagonal quasicrystal in the Al-Cu-Rh system with 56/38 atoms per thick/thin structural unit, based on 2092 unique reflections selected from the collected diffraction data, significantly improving the refinement results. The final R-factor value is 7.24%, which is over 0.5% better result comparing to originally reported. We believe our work will open a broader discussion on the disorder in quasicrystals (and other aperiodic systems) and motivate to develop new approaches to treat the diffraction data influenced by different types of disorder in the new way.