In prototyping complex systems, concept iterations often reach a point where incremental modifications to one part in a complex system can produce unexpected, cascading changes in the rest of the system. This phenomenon can require time-consuming and expensive corrections, particularly when physical prototypes are involved - as was the situation in the case study presented here. A design tool, the Design Structure Matrix (DSM), is commonly used to predict change propagation in complex designs. Using several examples, this paper illustrates situations where conventional DSMs fail to predict change propagation in the prototypes created during a robotic inspection system design project, due to complex interactions and system design constraints. The case study discussed here, a robotic inspection system for a nuclear waste storage cask, included interactions not easily captured in a conventional DSM. It was these interactions that interfered with the use of this tool to predict design change propagation. The paper then presents a method that was conceived to manage such changes; a way of modifying conventional DSMs to include design constraints and components. The case study examples show that the resulting technique, called the C+C DSM method, would have better predicted mid-development change propagation in the prototyping process.