Worked on issue #7. Issue should be fixed now.

plugin/src/main/java/net/jitse/npclib/plugin/NPCLibPlugin.java

@@ -40,6 +40,10 @@ public class NPCLibPlugin extends JavaPlugin implements Listener {
 
     @Override
     public void onDisable() {
+        if (npc != null) {
+            npc.destroy(false);
+        }
+
         getServer().getConsoleSender().sendMessage(ChatColor.BLUE + "[NPCLib] " + ChatColor.WHITE + "plugin disabled.");
     }
 

plugin/src/main/java/net/jitse/npclib/plugin/listeners/NPCListener.java

@@ -7,6 +7,7 @@ package net.jitse.npclib.plugin.listeners;
 import net.jitse.npclib.events.NPCDestroyEvent;
 import net.jitse.npclib.events.NPCInteractEvent;
 import net.jitse.npclib.events.NPCSpawnEvent;
+import net.jitse.npclib.events.trigger.TriggerType;
 import org.bukkit.ChatColor;
 import org.bukkit.event.EventHandler;
 import org.bukkit.event.Listener;
@@ -18,11 +19,19 @@ public class NPCListener implements Listener {
 
     @EventHandler
     public void onNPCSpawn(NPCSpawnEvent event) {
+        if (event.getTrigger() == TriggerType.AUTOMATIC) {
+            return;
+        }
+
         event.getPlayer().sendMessage(ChatColor.GREEN + "Spawned NPC " + event.getNPC().getEntityId());
     }
 
     @EventHandler
     public void onNPCDestroy(NPCDestroyEvent event) {
+        if (event.getTrigger() == TriggerType.AUTOMATIC) {
+            return;
+        }
+
         event.getPlayer().sendMessage(ChatColor.RED + "Destroyed NPC " + event.getNPC().getEntityId());
     }