The hexagonal-2H crystal phase of Ge recently emerged as a promising direct bandgap semiconductor in the mid-infrared range providing new prospects of additional opto-electronic functionalities of group-IV semiconductors (Ge and SiGe). The controlled synthesis of such hexagonal (2H) Ge phase is a challenge that can be overcome by using wurtzite GaAs nanowires as a template. However, depending on growth conditions, unusual basal stacking faults (BSFs) of I3-type are formed in the metastable 2H structure. The growth of such core/shell heterostructures is observed in situ and in real-time by means of environmental transmission electron microscopy using chemical vapour deposition. The observations provide direct evidence of a step-flow growth of Ge-2H epilayers and reveal the growth-related formation of I3-BSF during unstable growth. Their formation conditions are dynamically investigated. Through these in situ observations, we can propose a scenario for the nucleation of I3-type BSFs that is likely valid for any metastable hexagonal 2H or wurtzite structures grown on m-plane substrates. Conditions are identified to avoid their formation for perfect crystalline synthesis of SiGe-2H. This data set contains all the processed supporting videos of in-situ TEM observations .