If he was in a 1-seater, then why does he still have a NPC with him?
I assume you are in a 2-seater, if two of your 3 NPCs are missing.
This has nothing to do with the faction, Samuel. Fact is, the passenger capacity of the ship you entered was too little to support your and your entourage. If you want to have all of your NPCs with you, then you'll need to either:
-go back to where you and they were and get back out and wait for transport, or
-continue to your destination, then either
-go back and pick up the others one-by-one, or
-have someone with a ship with a larger passenger capacity pick them up for you and take them to where you are.