We have studied inhomogeneities in AlGaNiGaN heterostructures due to dislocations and limitations in the growth process. The electron occupancy in acceptor-like states along dislocations in wurtzite GaN were modelled. The reduction in free electron concentration and mobility was calculated as a function doping concentration, dislocation concentration and compensation. We also studied the mobility and PL-signal in heterostructures. Since the MBE growth takes place on insulating substrates, in a charged nitrogen plasma, effects due to substrate size may be expected. We report Hall effect measurements on Al0.2Ga0.8N/GaN HFET structure grown on 2 " sapphire and 1/4 and 1/8 pieces. The mobility was a factor of 2, larger on 2 " substrates compared to the pieces. Also photoluminescence variation that depend on substrate size and shape were presented.