When a pre-Maya 6.5 file that contains references is converted to a later version Maya file, a reference node named "_UNKNOWN_REF_NODE_" may be created and/or a special "_UNKNOWN_REF_NODE_" entry may be added to existing reference nodes.
This node type was used to store any edits that were made prior to 6.5 until those edits could be applied.
Once all references in the scene have been loaded, all edits should be applied and the _UNKNOWN_REF_NODE_ areas and nodes should disappear. If there are any edits which can not be applied (for example, nodes in the original reference file that were renamed or deleted), the _UNKNOWN_REF_NODE_ will remain in the file.
If you need to remove these reference nodes, you can do so by querying for the _UNKNOWN_REF_NODE_ and deleting it. That is, this specific node type cannot be deleted using the Reference Editor. In the Script Editor:
delete _UNKNOWN_REF_NODE_