Storing array of game objects in editor mode and click play corrupt the array.,Can't get game object from array after click on the start.

I am trying to store game objects in some array, but after the start button clicked all the game objects change and I can't get the references anymore from my array.
I am new in unity programming and all the changes I am doing are in the editor mode.. I am using editor class and call methods from OnInspectorGUI().

 [CreateAssetMenu(fileName = "Grid2D", menuName = "Grid/2D", order = 1)]
  public class Grid2D : ScriptableObject
     {
     private GameObject gridGameOject;
     public Transform[,] grid = new Transform[25, 25];
     public GameObject tile;
     void createTile(int x, int y)
             {
                 Vector3 position = Vector3.zero;
                 Bounds sprite_rendr = tile.GetComponent<SpriteRenderer>().bounds;
                 position.x = sprite_rendr.size.x*x;
                 position.y = sprite_rendr.size.y*y;
                 GameObject cube = (GameObject)PrefabUtility.InstantiatePrefab(tile);
                 cube.transform.SetParent(gridGameOject.transform, false);
                 cube.transform.localPosition = position;
                 grid[x, y] = cube.transform;
             }
     }