I mentioned this on the steam forums, but it has been buried.
There is an issue with how CE handles NPCs, currently when a player has moved out of range of an NPC, the server kills the npc. What this means is if you go back to where the NPC is, there will be a corpse of the dead npc. So for the NPC to appear again, the respawn timer has to tick down till the server respawns the NPC.
What should be happening is the NPC is despawned or put into an inactive state, so if the player comes back in range, that NPC is still alive.
I'm starting to see more people encountering this issue but they believe it is due to land claims/buildings even with no buildings.
To reproduce this, go to the black hand ship. Get one end of the ship's NPCs to spawn. Move to the other end, then come back to original end you were at. Either there will be corpses or no NPCs.
This only happens for NPCs, not animals or creatures to my knowledge.
EDIT: confirmed that it happens with animals and creatures as well.