Extensive geophysical surveys (MHVSR and MASW) conducted for the microzonation of the Kashmir Valley, Himalayas, revealed unexpected dynamic characteristics at certain sites pointing out the weak relationship between fundamental frequency (f0) and time-averaged shear wave velocity over 30 m depth (VS,30). Unusual low-frequency amplification at stiff soil sites and high-frequency amplification at weathered rock sites was obtained. On the contrary, high-frequency amplification was attained at a soft soil site over shallow bedrock. Instances of topographic amplification on slopes, hills, and valleys were encountered. Consequently, the commonly used VS,30-based single-proxy site classification failed to explain these atypical site effects, thus underscoring the caution to be exercised for site classification in geologically complex regions. These findings motivated the documentation of the anomalies and the search for the most suitable site characterisation scheme for the geological deposits of the Kashmir Valley. The coupled MHVSR-VS,30 proxy approach accomplished the best results for the study region.