The unique characteristics of a system-of-systems (SoS) environment pose many significant technical challenges when it comes to monitoring the behaviour of its component systems. In this collaborative environment, component misbehaviour is one of the most significant security threats. A key countermeasure is the ability to detect behaviour that could jeopardise the integrity, availability or functionality of either the composition or its components. However, due to the heterogeneity of the environment, as well as the uncertainty and dynamics of both the structure and function, component system behaviour is highly dynamic and unpredictable. This poses challenges for existing techniques and casts doubt over their reliability and effectiveness. Therefore potentially allowing behavioural threats to evade detection and yielding high false positive rates. In this paper, we will outline the security concerns that misbehaviour poses in terms of both individual components and the SoS as a whole. We will also propose our novel monitoring framework, which is designed to overcome the challenges of monitoring in a SoS environment. This paper also details our implementation and presents some of our initial results.