Design, construction and operation of building heating, ventilation and air conditioning (HVAC) systems are complicated processes that generally involve several stakeholders, such as mechanical designers, control system integrators, commissioning agents and facilities managers. It is important for all these stakeholders, at various phases of the project, to have a thorough understanding of the system components as well as the control strategy according to the design intent of the mechanical designers. For example, when assessing the behavior of an HVAC system during operation phase, it is important for facilities managers to check for the correctness of every component's behavior and its control logic against the design specifications. The control sequences and logic of HVAC systems are primarily conveyed through schematic diagrams and textual descriptions called "sequence of operations" (SOOs) in construction documents (ASHRAE, 2004). Several challenges are associated with extracting and interpreting the information contained in these SOOs. Through a detailed analysis of a case-study conducted in relation to the information provided in the SOOs for the air handling unit (AHU) in a building, the research described in this paper highlights these challenges. Challenges such as missing information for controlled parameters, as well as textual descriptions that are open to interpretations, are common and result in inaccurate interpretation of the system behavior. This may adversely affect the overall performance of systems and lead to energy inefficiencies.