Unexpected neutral defenders

[Norfleet]

Victory points can exist even if they cannot win the game: They're set into the map file and occur even when victory by holding of victory points doesn't exist. The provinces will retain their special sites, although no victory is attained by holding any or all.

As for independent resistance, are you certain the game was started on indy-5, and not a higher setting? If you were not the one who started the game, it's also possible that your friend has Poked his map file in a manner similar to Gandalf's Poke in the Eye map: The map file and settings of the host is used when the game is generated, not yours.