The experimental x-ray diffraction patterns of a Si$_{0.4}$Ge$_{0.6}$/Si(001) epitaxial film with a low density of misfit dislocations are modeled by the Monte Carlo method. It is shown that an inhomogeneous distribution of 60$^circ$ dislocations with dislocations arranged in bunches is needed to explain the experiment correctly. As a result of the dislocation bunching, the positions of the x-ray diffraction peaks do not correspond to the average dislocation density but reveal less than a half of the actual relaxation.