Safety Instrumented Systems (SIS) protect major hazard facilities, e.g. power plants, against catastrophic accidents. An SIS consists of hardware components and a controller software -- the ``program''. Current safety analyses of SIS' include the construction of a fault tree, summarising potential faults of the components and how they can arise within an SIS. The exercise of identifying faults typically relies on the experience of the safety engineer. Unfortunately the program part is often too complicated to be analysed in such a ``by hand" manner and so the impact it has on the resulting safety analysis is not accurately captured. In this paper we demonstrate how a formal model for faults and failure modes can be used to analyse the impact of an SIS program. We outline the underlying concepts of \emph{Failure Mode Reasoning} and its application in safety analysis, and we illustrate the ideas on a practical example.