Nonlinear networked systems are of interest in several areas of research, such as multi-agent systems and social networks. In this paper, we examine the controllability of several classes of nonlinear networked dynamics on which the underlying graph admits negative weights. Such signed networks exhibit bipartite clustering when the underlying graph is structurally balanced. We show that structural balance is the key ingredient inducing uncontrollability when combined with a leader-node symmetry and a certain type of dynamical symmetry. We then examine the problem of extracting the bipartite structure of such graphs from data using Extended Dynamic Mode Decomposition to approximate the corresponding Koopman operator.