That's because the NPC's are ship instanced, so when you leave your ship that instance closes and the on foot instance takes over where you might instance with other players in the fleet carrier interior. If they kept both instances running you might not be able to instance with any on foot CMDRS if there were a lot of in ship CMDRS hanging around. Not sure how they will get around that one.
I've noticed the same thing happens in station concourses too. Whenever I disembark after landing at a station, I have to rush to the concourse window immediately if I want a chance to catch the last NPCs leaving, and then nothing.
It's even worse if you log in on-foot to a concourse. Not one ship, even if I sit there for a good 20 minutes
(yes, I do that sometimes, it's nice to just chill and enjoy the bar ambience once in a while).
And they made such a huge deal about being able to watch ships dock and undock from the bar, but it's virtually non-existent.