The introduction of complex network concepts in the study of transportation systems has supposed a paradigm shift and has allowed understanding different transport phenomena as the emergent result of the interactions between the elements composing them. In spite of several notable achievements, lurking pitfalls are undermining our understanding of the topological characteristics of transportation systems. In this study, we analyse four of the most common ones, specifically related to the assessment of the scale-freeness of networks, the interpretation and comparison of topological metrics, the definition of a node ranking, and the analysis of the resilience against random failures and targeted attacks. For each topic we present the problem from both a theoretical and operational perspective, for then reviewing how it has been tackled in the literature and finally proposing a set of solutions. We further use six real-world transportation networks as case studies and discuss the implications of these four pitfalls in their analysis. We present some future lines of work that are stemming from these pitfalls and that will allow a deeper understanding of transportation systems from a complex network perspective.