We report an intriguing anomalous behavior observed in the temperature-dependent Raman spectra of mono-, bi-, and trilayer molybdenum disulfide samples with sulfur vacancies, measured at high temperatures ranging from room temperature to 463 K. In contrast to existing reports, we observed a decrease in the FWHM of the A\(_{1g}\) phonon mode, along with an increase in the relative intensity of the A\(_{1g}\) mode to the E\(_{2g}^1\) mode, as the temperature increased. This trend becomes less prominent as the layer number increases from monolayer, disappearing entirely in few-layer samples. Additionally, we observed an intensity enhancement in the photoluminescence spectra of MoS₂ samples at high temperatures (up to 550 K), which depends on the layer number. These observations are explained by considering the presence of sulfur vacancies, their interaction with the environment, electron density reduction, and a phonon-mediated intervalley charge transfer at elevated temperatures. Our results unambiguously establish that the effect of defects (sulfur vacancies) is more prominently reflected in the temperature dependence of FWHM and the relative intensity of the Raman modes rather than in the Raman peak positions.