This tool first assesses whether there are any isolated groups of features based on the Spatial Constraints specified. Clustering begins with disconnected groups of features already forming clusters.
The Spatial Constraints parameter determines which features can be clustered together. If you see a message about groups of disconnected clusters, you may want to modify your Spatial Constraints parameter. More information on how the Spatially Constrained Multivariate Clustering tool works with disconnected groups of features is described in the tool help. Creating a spatial weights matrix using K nearest neighbors and increasing the Number of Neighbors parameter until there are no more disconnected groups of features will ensure that both spatial and data relationships are incorporated into the clustering algorithm.