We report the characterization by Raman spectroscopy of rutile nanocrystals embedded in cluster-assembled TiO2 films produced by supersonic cluster beam deposition. Thermal annealing of the as-deposited films promotes the growth of rutile and anatase nanoparticles with a dimension distribution peaked around 10 nm. We show that a phonon confinement model is not adequate to explain the features of the lattice dynamics of rutile nanocrystals. The coexistence of the two crystalline phases allows us to identify the role of chemical and structural inhomogeneities in the film potentially affecting the Raman spectra. Our results suggest that the lattice dynamics of rutile nanocrystals is influenced by the dielectric constant of the cluster-assembled films.