store instantiated in Array. c#

Length property returns number of elements in the array. If you create one-dimensional array, e.g. someArray[10], then length of dimension 0 (zero) is 10, and it is equal to Length of the whole array. If you create two-dimensional array, e.g. someArray[10,5], then length of dimension 0 is 10, length of dimension 1 is 5, and Length will return 50. You can get the length of given dimension by using GetLength(dimension) method.

In your case, you have three dimensional array, so Length is returning 100*20*100, so your random ranges from 0 to 199999. You have to do:

 var randomX = Random.Range(0, CubeCount.GetLength(0) - 1);
 var randomY = Random.Range(0, CubeCount.GetLength(1) - 1);
 var randomZ = Random.Range(0, CubeCount.GetLength(2) - 1);
 
 var randomElement = CubeCount[randomX, randomY, randomZ];

EDIT:

Ok - after all the comments, I think I now get the gist of your problem, although I have to admit it would be hard without image :)

You want to have a terrain 32x32 tiles with random heights, and then you want to generate ore (or anything else) on top of random tile. Correct me if I'm wrong :)

If the above is ok, then I'd do it that way:

 using UnityEngine;
 
 public class TileGen : MonoBehaviour {
     
     public GameObject cubePrefab;
     int chunkheightmapWidth = 32;
     int chunkheightmapHeight = 32;
     public float EpicGenerator;
     public float Tiling = 10.0f; 
     
     // two dimensional array of items - storing in one dimensional is also possible, but not the way you did
     public GameObject[,] items;
     // small addition, to check if given coordinates was already used
     private bool[,] alreadyGenerated;
     
     void Start()
     {
         EpicGenerator = Random.Range(0.8f, 1.9f);
         GenerateItems(Tiling);
     }
      
     void Update()
     {
         if(Input.GetKeyDown(KeyCode.I))
         {
             var randomX = Random.Range(0, items.GetLength(0) - 1);
             var randomZ = Random.Range(0, items.GetLength(1) - 1);
             print("x: " + randomX + ", z: " + randomZ);
             GenerateOre(randomX, randomZ);
         }
     }
     
     private void GenerateOre(int x, int z)
     {
         if(alreadyGenerated[x, z])
         {
             Debug.Log ("already generated at this location");
             return;
         }
         
         // get item on top of which you want to create ore
         var item = items[x,z];
         var ore = GameObject.CreatePrimitive(PrimitiveType.Sphere);
         ore.transform.position = item.transform.position + new Vector3(0, item.transform.localScale.y, 0);
         alreadyGenerated[x, z] = true;
     }
     
     public void GenerateItems(float tileSize)
     {
         items = new GameObject[chunkheightmapWidth, chunkheightmapHeight];
         alreadyGenerated = new bool[chunkheightmapWidth, chunkheightmapHeight];
         
         for (int x = 0; x < chunkheightmapWidth; x++)
         {
             for (int z = 0; z < chunkheightmapHeight; z++)
             {
                 var height = Mathf.PerlinNoise(((float)x / (float)chunkheightmapWidth) * tileSize, ((float)z / (float)chunkheightmapHeight) * tileSize)/EpicGenerator;
                 var item = (GameObject)Instantiate(cubePrefab, new Vector3(x, height, z), Quaternion.identity);
                 item.transform.parent = transform;
                 items[x,z] = item;
                }
         }
     }
 }

If it's ok, but you don't have a clue why some part of it works, please let me know, as I want you to understand this.