It is well-known that mechanical properties of gels are strongly related to inhomogeneities of gels such as spatial and connectivity inhomogeneities (defects and variation of cycles). Here, a cycle is defined as the type of polygonal shape formed by several prepolymers. However, these inhomogeneities, especially connectivity inhomogeneities, have hardly been quantified due to the difficulty in directly observing them. To directly observe and analyze gel structures, we used a molecular dynamics simulation to reproduce gelation process and quantified defects and cycles of the obtained gels. Furthermore, we investigated the relation between defects or cycles and spatial inhomogeneities. Our investigation indicated that defects caused spatial inhomogeneities in dilute and semidilute systems. On the other hand, in concentrated systems, self-biting links, in which a cross-link connects with itself, caused spatial inhomogeneities. This could be observed in the swollen state, which is revealed in the difference in degree of swelling of cycles during the swelling process.