In this work we analyze a phenomenon that takes place when growing magnetron sputtered porous/compact multilayer systems by alternating the oblique angle and the classical configuration geometries. We show that the compact layers develop numerous fissures rooted in the porous structures of the film below, in a phenomenon that amplifies when increasing the number of stacked layers. We demonstrate that these fissures emerge during growth due to the high roughness of the porous layers and the coarsening of a discontinuous interfacial region. To minimize this phenomenon, we have grown thin interlayers between porous and compact films under the impingement of energetic plasma ions, responsible for smoothing out the interfaces and inhibiting the formation of structural fissures. This method has been tested in practical situations for compact TiO2/porous SiO2 multilayer systems, although it can be extrapolated to other materials and conditions.