Accessing the array of a null item / Moving items in array

I am new to unity and starting to make my own small little game. Right now using c#, and I am trying to make a Match3 Game. Currently have problem making the gems/tiles dropping down. I am able to destroy the gem. I am able to use the Coroutine to check if the array is null (access from another script). However I cannot seem to get the gems to drop down, or move the items in the array. think I am not accessing/identifying the actual null tile in the gem Holder correctly. Below is the error I get for the Coroutine

" NullReferenceException: Object reference not set to an instance of an object MouseManager.MouseOverGem (UnityEngine.GameObject ourHitObject) (at Assets/Scripts/MouseManager.cs:127) MouseManager.Update () (at Assets/Scripts/MouseManager.cs:56) "

 public Vector2 mapSize;
 private Vector3 gridPlacement;

 public GameObject[] listGems;
 public GameObject gem;
 public GameObject[,] gemHolder;


 void Start()
 {
     //allGems = new GameObject[mapSize.x, mapSize.y];
     GenerateBoard();

 }

 public void GenerateBoard()
 {
     gemHolder = new GameObject[9, 9];
     // putting the board into a parent
     string holderName = "Generated Board";
     Transform boardHolder = new GameObject(holderName).transform;
     boardHolder.parent = transform;

     for (int x = 0; x < mapSize.x; x++)
     {
         for (int y = 0; y < mapSize.y; y++)
         {
             gridPlacement = CoordToPosition(x, y);

             int gemsToUse = Random.Range(0, listGems.Length); // making gems random
             gem = Instantiate(listGems[gemsToUse], gridPlacement, Quaternion.Euler(Vector3.right * 90)); // putting gems in the board

             gem.transform.parent = this.transform; // putting it in parent
             gem.name = "(" + x + "," + y + ")"; // naming the grid as coordinates
             //make sure tile is aware of its placement on the map
             gem.GetComponent<GemPosition>().x = x;
             gem.GetComponent<GemPosition>().y = y;

             gemHolder[x, y] = gem;

         }
     }
 }

 Vector3 CoordToPosition(int x, int y)
 {
     return new Vector3(-mapSize.x / 2 + 3f + x, 0, -mapSize.y / 2 + 0.5f + y); // position of grid
 }

 public IEnumerator MoveRowsDown()
 {
     int nullCount = 0;
     for (int x = 0; x < mapSize.x; x++)
     {
         for (int y = 0; y < mapSize.y; y++)
         {
             if (gemHolder[x, y] == null)
             {
                 nullCount++;
             }
             else if (nullCount > 0)
             {
                 gemHolder[x, y] = gemHolder[x, (y - nullCount)];
             }
         }
         nullCount = 0;
     }
     yield return new WaitForSeconds(.4f);
 }