Same situation on our server.
Joined Pirate faction to test a few things but didn\'t immediately lose the faction when I left. In fact, was able to initiate_waves a number of times between leaving the faction and it becoming unknown.
Now.. /initate_wave still spawns ships that are under AI control, but they fly in, poke around without attacking, then leave. All bear an \"(unknown faction -1)\" tag.
So the server still has an NPC group to spawn from, but it\'s not registered as a faction anymore. Need a way to reinstate without a reinstall, but without more info I\'m afraid that\'s my only option.