An extended formation of faceted pit-like defects on Ge(0 0 1) and Ge(1 1 1) wafers was obtained by thermal cycles to T > 750 degrees C. This temperature range is relevant in many surface-preparation recipes of the Ge surface. The density of the defects depends on the temperature reached, the number of annealing cycles performed and correlates to the surface-energy stability of the specific crystal orientation. We propose that the pits were formed by preferential desorption from the strained regions around dislocation pile-ups. Indeed, the morphology of the pits was the same as that observed for preferential chemical etching of dislocations while the spatial distribution of the pits was clearly non-Poissonian in line with mutual interactions between the core dislocations.