In situ reflection high-energy electron diffraction, atomic force microscopy and photoluminescence spectroscopy have been combined to analyze the kinetics of the growth mode transition in the Ge/Si(001) system. By performing experiments in the dynamic growth regime and under growth interruption, we clearly establish the existence of intermediate clusters. We show that these clusters are metastable both in view of structural and optical properties. In particular, experiments performed with growth interruption have revealed that the two-dimensional wetting layers undergo a morphological instability well before reaching the critical thickness.