Previous research has shown that individuals fail to understand the basic building blocks of complex systems such as stocks and flows, feedbacks, and time delays. This paper presents three empirical studies intended to understand why individuals misperceive the relationships between stocks and flows. We used problems that were quite familiar to the participants, interventions to motivate participants to think harder in the problem, simplifications of graphs and direction of attention to specific aspects of the graphs. The results seem to disclose some of the mechanisms that individuals use to make their inferences about the graphs. That is, individuals attend to the most salient features of the graphical representation to make their inferences about the stock in the task. Does this really imply a misunderstanding of stocks and flows?  We believe the further research needs to address this problem in realistic presentations rather than graphical representations.