In this study, possible origins of small V-pits observed in multiple quantum wells (MQWs) overgrown on as-grown and porosified InGaN superlattice (SL) pseudo-substrates have been investigated. Various cross-sectional transmission microscopy techniques revealed that some of the small V-pits arise from the intersection of threading defects with the sample surface, either as part of dislocation loops or trench defects. Some small V-pits without threading defects are also observed. Energy dispersive x-ray study indicates that the Indium content in the MQWs increases with the averaged porosity of the underlying template, which may either be attributed to a reduced compositional pulling effect or the low thermal conductivity of the porous layer. Furthermore, the porous structure inhibits the glide or extension of the misfit dislocations (MD) within the InGaN SL. The extra strain induced by the higher Indium content and the hindered movement of the MDs combined may explain the observed additional small V-pits present on the MQWs overgrown on the more relaxed templates.