Systems engineering and development of system dynamics models are strongly interconnected. During this process of system construction, system dynamics modelling represents a useful approach to simulation of system behaviour over time and to support the quality and suitability of related decision. Appropriate application of systems thinking during the whole modelling process plays a crucial role and it is both problematic and challenging. This paper focuses on the identification of the issues occurring during the modelling process. The applied methods incorporates the experimental set-up, direct observation of modellers and qualitative analysis of developed models. Consequently, the list of identified drawbacks linked with particular systems thinking track is developed. The identified mistakes together with their linkage with type of thinking are summarised in a useful overview of what could and should be omitted or eliminated during the system dynamics modelling. Results reveal that operational thinking represents the most challenging thinking track. It is followed by non-linear, analytical, critical and structural thinking. Based on the achieved results, the modellers could analyse and revise their approaches and thinking patterns. These can be reconsidered and appropriately adapted following the principles of the correct application of systems thinking during system dynamics modelling.