Defects can significantly affect performance of nanopatterned magnetic devices, therefore their influence on the material properties has to be understood well before the material is used in technological applications. However, this is experimentally challenging due to the inability of the control of defect characteristics in a reproducible manner. Here, we construct a micromagnetic model, which accounts for intrinsic and extrinsic defects associated with the polycrystalline nature of the material and with corrugated edges of nanostructures. The predictions of the model are corroborated by the measurements obtained for highly ordered arrays of circular Co/Pd antidots with perpendicular magnetic anisotropy. We found that magnetic properties, magnetic reversal and the evolution of the domain pattern are strongly determined by density of defects, heterogeneity of nanostructures, and edge corrugations. In particular, an increase in the Néel domain walls, as compared to Bloch walls, was observed with a increase of the antidot diameters, suggesting that a neck between two antidots can behave like a nanowire with a width determined by the array period and antidot size. Furthermore, the presence of edge corrugations can lead to the formation of a network of magnetic bubbles, which are unstable in non-patterned flat films.