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We investigated the temperature-dependence of the Raman spectra of a nine-layer BaRuO$_3$ single crystal and a four-layer BaRuO$_3$ epitaxial film, which show pseudogap formations in their metallic states. From the polarized and depolarized spectra, the observed phonon modes are assigned properly according to the predictions of group theory analysis. In both compounds, with decreasing temperature, while $A_{1g}$ modes show a strong hardening, $E_g$ (or $E_{2g}$) modes experience a softening or no significant shift. Their different temperature-dependent behaviors could be related to a direct Ru metal-bonding through the face-sharing of RuO$_6$. It is also observed that another $E_{2g}$ mode of the oxygen participating in the face-sharing becomes split at low temperatures in the four layer BaRuO$_3 $. And, the temperature-dependence of the Raman continua between 250 $\sim $ 600 cm$^{-1}$ is strongly correlated to the square of the plasma frequency. Our observations imply that there should be a structural instability in the face-shared structure, which could be closely related to the pseudogap formation of BaRuO$_3$ systems., Comment: 8 pages, 6 figures. to be published in Phys. Rev. B