From the SVRF Manual, "LVS Circuit Extraction Messages" section:
WARNING: Top level port name “<name>” on net <id> at location (x,y) already used on net <id>; ignored.
This warning indicates a top-level port naming conflict in the hierarchical SPICE netlister. This occurs when two or more nets are connected to top-level-cell ports with identical names. The warning appears only when the port names would have been otherwise used for netlisting. Specifically, the two nets in question must be unnamed or must have names that are not valid for netlisting, and the port name must be valid for netlisting. The hierarchical SPICE netlister uses the port name to identify one of the nets and its port, and uses the internal number of the other net to identify that net and its port. The net that receives the port name is chosen arbitrarily. This message occurs when LVS Netlist Connect Port Names YES is specified.
Your rule file specifies that this situation be flagged with a warning. There are two choices to rectify it. 1) Set LVS Netlist Connect Port Names NO (the default). 2) Name the nets differently that give the port names.