Question Instantiated cube prefab different Y value than vertex created as same location with same Y value?

Code (CSharp):

1. using System.Collections;
2. using System.Collections.Generic;
3. using UnityEngine;
4. using Ex = System.Exception;
5.  
6. public class TerrainGen : MonoBehaviour
7. {
8.     public int width = 16;
9.     public int height = 50;
10.  
11.     public GameObject myPrefab;
12.  
13.     private MeshFilter meshFilter;
14.     private static float noiseScale = .05f;
15.  
16.     Mesh mesh;
17.     Vector3[] vertices;
18.     int[] triangles;
19.  
20.     void Start()
21.     {
22.  
23.         GeneratePerlinNoiseMesh(0, 0);
24.     }
25.  
26.     public void GeneratePerlinNoiseMesh(int offsetX, int offsetZ) {
27.         mesh = new Mesh();
28.         GetComponent<MeshFilter>().mesh = mesh;
29.         vertices = new Vector3[(width+1) * (width+1)];
30.         for (int i = 0, x = 0; x <= width; x++) {
31.             for (int y = 0; y <= height; y++) {
32.                 for (int z = 0; z <= width; z++) {
33.                     if (getBlock(x + offsetX * width, y, z + offsetZ * width) && (!isSurrounded(x + offsetX * width, y, z + offsetZ * width))) {
34.                         Debug.Log(y);
35.                         GameObject cube = Instantiate(myPrefab, new Vector3(x + offsetX * width, y, z + offsetZ * width), Quaternion.identity);
36.                  
37.                         Debug.Log(i + "" +  new Vector3(x, y, (i%(width + 1))));
38.                         vertices[i] = new Vector3(x, y, (i%(width + 1)));
39.                         i++;
40.                     }
41.                 }
42.             }
43.  
44.         }
45.         triangles = new int[width * width* 6];
46.  
47.         int vert = 0;
48.         int tris = 0;
49.  
50.         for (int x = 0; x < width; x++) {
51.             for (int z = 0; z < width; z++) {
52.                 triangles[tris + 0] = vert + 0;
53.                 triangles[tris + 2] = vert + width + 1;
54.                 triangles[tris + 1] = vert + 1;
55.                 triangles[tris + 3] = vert + 1;
56.                 triangles[tris + 5] = vert + width + 1;
57.                 triangles[tris + 4] = vert + width + 2;
58.  
59.                 vert++;
60.                 tris += 6;
61.             }
62.             vert++;
63.         }
64.         UpdateMesh();
65.     }
66.  
67.     void UpdateMesh() {
68.  
69.         mesh.Clear();
70.  
71.         mesh.vertices = vertices;
72.         mesh.triangles = triangles;
73.  
74.         mesh.RecalculateNormals();
75.     }
76.  
77.     public static bool getBlock(int x, int t, int z) {
78.         float density = ((Perlin3D(x * noiseScale, t * noiseScale, z * noiseScale)*2)-1);
79.         float yAverage = (t*2) / 100.0f;
80.         yAverage = (yAverage * 2) - 1;
81.  
82.         //Increase yAverage divison for more moutains, decrease for flatter
83.         density = (density + (yAverage/1.2f)) / 2;
84.         if (density >= 0) {
85.             return true;
86.         } else {
87.             return false;
88.         }
89.  
90.     }
91.     public static float Perlin3D(float x, float t, float z) {
92.         float ab = Mathf.PerlinNoise(x, t);
93.         float bc = Mathf.PerlinNoise(t, z);
94.         float ac = Mathf.PerlinNoise(x, z);
95.  
96.         float ba = Mathf.PerlinNoise(t, x);
97.         float cb = Mathf.PerlinNoise(z, t);
98.         float ca = Mathf.PerlinNoise(z, x);
99.  
100.         float abc = ab + bc + ac + ba + cb + ca;
101.         return abc / 6f;
102.     }
103.  
104.     bool isSurrounded(int x, int t, int z) {
105.         int[] dx = {-1, 1, 0, 0, 0, 0};
106.         int[] dy = {0, 0, -1, 1, 0, 0};
107.         int[] dz = {0, 0, 0, 0, -1, 1};
108.  
109.         for (int i = 0; i < 6; i++) {
110.             if (!getBlock(x + dx[i], t + dy[i], z + dz[i])) {
111.                 return false;
112.             }
113.         }
114.  
115.         return true;
116.     }
117.  
118. }

In my GeneratePerlinNoiseMesh function I instantiate the cube object using
Instantiate(myPrefab, new Vector3(x + offsetX * width, y, z + offsetZ * width), Quaternion.identity);. After I create a vertex at the same location as the cube using
vertices = new Vector3(x, y, (i%(width + 1)));. If you look at the image Debug.Log(i + "" + new Vector3(x, y, (i%(width + 1)))); outputs y value is 22 for vertex number 18 and Debug.Log(y); is also outputting 22 yet the position y for the cube instantiated at the same X and Z position is 23 using the same y variable as the vertex? Both X and Z are the same for all vertices but the y value is 1 off for some of them like showed in the image... anyone know the problem here? I have tried multiple different strategies to fix it and have spent plenty of time looking at the code with no success.