Understanding logical network connectivity is essential in network topology mapping especially in a fast growing network where knowing what is happening on the network is critical for security purposes and where knowing how network resources are being used is highly important. Mapping logical communication topology is important for network auditing, network maintenance and governance, network optimization, and network security. However, the process of capturing network traffic to generate the logical network topology may have a great influence on the operation of the network. In hierarchically structured networks such as control systems, typical active network mapping techniques are not employable as they can affect time-sensitive cyber-physical processes, hence, passive network mapping is required. Though passive network mapping does not modify or disrupt existing traffic, current passive mapping techniques ignore many practical issues when used to generate logical communication topologies. In this paper, we present a methodology which compares topologies from an idealized mapping process with what is actually achievable using passive network mapping and identify some of the factors that can cause inaccuracies in logical maps derived from passively monitored network traffic. We illustrate these factors using a case study involving a hierarchical control network.