High resolution double axis X-ray diffractometry has been undertaken on InGaAs/AlGaAs strained layer epitaxial systems on (001) GaAs substrates. A clear set of fringes has been identified which arises due to the presence of an imperfect layer at the interface between the GaAs substrate and the undoped GaAs epitaxial buffer layer. The period corresponds to the Pendellosung period for the whole epitaxial layer stack. These fringes have very low contrast and are not present in all specimens studied. Detailed simulations have been undertaken assuming a thin interfacial layer of GaAs with a different lattice parameter to the substrate. The system is equivalent to a Bragg case X-ray interferometer. Fringe amplitude is found to vary linearly with interface layer thickness and increases with mismatch of this layer. A good match between experiment and simulation was obtained for a 1 nm layer mismatched by 3000 ppm. The presence of such a layer, probably GaCxAsl-x has been confirmed by transmission electron microscopy. We show that highly sh'rained layers of this thickness between layers over 1 micron in thickness can lead to splitting of high intensity layer peaks, giving rise to possible misinterpretation of data.