Failure Modes and Effects Analysis (FMEA) is the process of identifying potential failure modes, their causes and effects associated with a product, process or system. In this paper, we discuss the application of FMEA in the design of cybersecurity experiments using a medium interaction server honeypot in an Internet of Things (IoT) environment. Through FMEA analysis, we identify the factors affecting the outcome or contributing to the potential failures of the cybersecurity experiment. We discuss the causes of failures, their effects and how to minimise or mitigate them.