SiGe/Si heterostructures grown by ion beam sputter deposition were characterized by high-resolution X-ray diffraction and transmission electron microscopy. Agglomerates of point defects, formed under ion bombardment during growth, were observed in electron microscopy images. These specific defects resulted in structural disorder which could be described in terms of local fluctuations of interplanar distances. The averaged magnitudes of the fluctuations were derived from X-ray diffraction spectra using a novel simulation procedure based on the direct summation of scattered waves in imperfect heterostructures. This approach allowed us to characterize quantitatively the degree of the structural disorder, and to follow defect transformations as a function of growth and annealing temperatures.