The missing reference warning is shown in a sync when an entity was referenced but could not be found.
This warning can be best described by an example.
Consider the relationship between an Application model and an Application Stage model. During a sync, the Application model will create a reference to the entity in the Application Stage model to determine which stage it is in (also known as Application Status). If, later in the sync, that entity cannot be found in the Application Stage model, it is referred to as a missing, floating, or dangling reference. This situation may occur because the referenced entity was deleted or could not be fetched due to insufficient permissions.
For some tools, this is expected.