How to prevent prefab of custom editor inspector from overriding array size.

I created a custom editor for the inspector of one of my scripts. The issue is, when I create a prefab of an object with the script attached, the prefab's array will override the array of every instance to be the same.

What causes this and how can I prevent it?

EDIT: I am running unity version 5.6.2f1

Editor Code:

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 using UnityEditor;
 
 
  [CustomEditor(typeof(PointMovingPlatform))]
 public class PointMovingPlatformEditor : Editor {
 
     PointMovingPlatform pmp;
 
     public void OnEnable()
     {
         pmp = (PointMovingPlatform)target;
     }
 
     public override void OnInspectorGUI()
     {
         ///////////////////////////////////////
         //Display speed 
         ///////////////////////////////////////
         pmp.speed = EditorGUILayout.FloatField("Speed", pmp.speed);
         GUILayout.Space(20);
 
         /////////////////////////////////////////
         //Display waypoints array
         // - Allow adding/removing of points
         /////////////////////////////////////////
 
         if (GUILayout.Button("Add Waypoint"))
         {
             AddWaypoint();
         }
 
         for (int i = 0; i < pmp.waypoints.Count; i++)
         {
             GUILayout.BeginHorizontal();
 
             GUILayout.Label("Waypoint " + i.ToString());
             GameObject old = pmp.waypoints[i];
             pmp.waypoints[i] = (GameObject)EditorGUILayout.ObjectField(pmp.waypoints[i], typeof(GameObject), true);
             if(old != pmp.waypoints[i])
             {
                 if(old.name == "Waypoint")
                     DestroyImmediate(old);
             }
             if (GUILayout.Button("[X]"))
             {
                 RemoveWaypoint(i);
             }
 
             GUILayout.EndHorizontal();
         }
 
         //Display original for reference
         GUILayout.Space(40);
         GUILayout.Label("ORIGINAL INSPECTOR");
         base.OnInspectorGUI();
     }
 
     void AddWaypoint()
     {
         GameObject newWP = new GameObject("Waypoint");
         newWP.transform.position = new Vector3(pmp.platform.transform.position.x, pmp.platform.transform.position.y, pmp.platform.transform.position.z);
         newWP.transform.parent = pmp.transform;
         pmp.waypoints.Add(newWP);
     }
 
     void RemoveWaypoint(int index)
     {
         DestroyImmediate(pmp.waypoints[index].gameObject);
         pmp.waypoints.RemoveAt(index);
     }
 }
 

Script:

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 
 public class PointMovingPlatform : MonoBehaviour {
 
     public float speed;
 
     public GameObject platform;
 
     public List<GameObject> waypoints;
     //public Transform[] waypoints;
 
     private Vector3 direction;
     private Transform destination;
 
     private int currentWaypoint = 0;
     
     void Start () {
         if(waypoints.Count > 0)
         {
             destination = waypoints[currentWaypoint].transform;
             direction = (destination.position - platform.transform.position).normalized;
         }
     }
 
     void Update()
     {
         platform.transform.Translate(direction * speed * Time.deltaTime);
 
         float distance = Vector3.Distance(platform.transform.position, destination.position);
         if (distance < speed * Time.deltaTime || distance < speed / 20f)
         {
             platform.transform.position = destination.transform.position;
 
             NextDestination();
 
         }
     }
 
     private void OnDrawGizmos()
     {
         for(int i = 0; i < waypoints.Count; i++)
         {
             Gizmos.color = Color.grey;
             Gizmos.DrawWireCube(waypoints[i].transform.position, platform.transform.localScale);
 
             Gizmos.color = Color.black;
             if(i + 1 >= waypoints.Count)
             {
                 Gizmos.DrawLine(waypoints[waypoints.Count - 1].transform.position, waypoints[0].transform.position);
             } else
             {
                 Gizmos.DrawLine(waypoints[i].transform.position, waypoints[i + 1].transform.position);
             }
 
             if(waypoints.Count > 0)
             {
                 Gizmos.DrawLine(platform.transform.position, waypoints[currentWaypoint].transform.position);
             }
         }
     }
 
     void NextDestination()
     {
         if (waypoints.Count > 0)
         {
             currentWaypoint++;
             if(currentWaypoint >= waypoints.Count)
             {
                 currentWaypoint = 0;
             }
             destination = waypoints[currentWaypoint].transform;
             direction = (destination.position - platform.transform.position).normalized;
         }
     }
 
 }
 

I apologize for the large amount of code, but I just want to ensure there is enough content to determine why this issue arises. Thank you in advance.