We still do not have clear figure about how software systems evolve and how we may control its evolution process. Software structure has been identified that may have the biggest impact, especially because it may be represented from numerous perspectives. Novelty introduced in this paper is the way how we define the structure of evolving complex software systems. The structure is represented with help of graph representations, and subgraph frequencies, the concept reused from the network analysis theory. The graph structure of a software system and its evolution over the system versions, as well as its relation to defectiveness, is empirically studied in terms of subgraph frequencies and motifs for more than 30 releases of three large open source software systems. We identified that the same set of subgraphs of software system is present across the system version, but different sets, although overlapping, are present in different software systems. Furthermore, we confirmed the continuous system evolution in terms of continuous structure change and we find some evidence for its relation to system defectiveness.