Hi, the issue reported is not a bug with the engine but the provided script is not mapping the UV's correctly.

Changing the provided function as follows does resolve the problem:

public static GameObject multiTextures(string sideID, string topID, string bottomID)
{
GameObject model = GameObject.CreatePrimitive(PrimitiveType.Cube);
Material material = new Material(Shader.Find("Standard"));

Texture2D side = Resources.Load<Texture2D>("Texture/Block/" + sideID);
Texture2D top = Resources.Load<Texture2D>("Texture/Block/" + topID);
Texture2D bottom = Resources.Load<Texture2D>("Texture/Block/" + bottomID);

Texture2D textureAtlas = new Texture2D(32, 32, TextureFormat.RGB24, false);
textureAtlas.filterMode = FilterMode.Point;
textureAtlas.wrapMode = TextureWrapMode.Clamp;

Texture2D[] textures = { side, top, bottom };
Rect[] atlasUVs = textureAtlas.PackTextures(textures, 0);
byte[] bytes = textureAtlas.EncodeToPNG();
System.IO.File.WriteAllBytes(Application.dataPath + "/Resources/Texture/BlockAtlas.png", bytes);

material.mainTexture = textureAtlas;
material.SetFloat("_Metallic", 0);
material.SetFloat("_Glossiness", 0);

MeshRenderer meshRenderer = model.GetComponent<MeshRenderer>();
meshRenderer.material = material;
Mesh mesh = model.GetComponent<MeshFilter>().mesh;
Vector2[] UVs = new Vector2[mesh.vertices.Length];

// South (front)
UVs[0] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMin);
UVs[1] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMin);
UVs[2] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMax);
UVs[3] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMax);

// Top
UVs[4] = new Vector2(atlasUVs[1].xMin, atlasUVs[1].yMin);
UVs[5] = new Vector2(atlasUVs[1].xMin, atlasUVs[1].yMax);
UVs[8] = new Vector2(atlasUVs[1].xMax, atlasUVs[1].yMin);
UVs[9] = new Vector2(atlasUVs[1].xMax, atlasUVs[1].yMax);

// North (back)
UVs[6] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMin);
UVs[7] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMin);
UVs[10] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMax);
UVs[11] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMax);

// Bottom
UVs[15] = new Vector2(atlasUVs[2].xMin, atlasUVs[2].yMin);
UVs[14] = new Vector2(atlasUVs[2].xMin, atlasUVs[2].yMax);
UVs[12] = new Vector2(atlasUVs[2].xMax, atlasUVs[2].yMin);
UVs[13] = new Vector2(atlasUVs[2].xMax, atlasUVs[2].yMax);

// West (left)
UVs[19] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMin);
UVs[18] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMax);
UVs[16] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMin);
UVs[17] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMax);

// East (right)
UVs[23] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMin);
UVs[22] = new Vector2(atlasUVs[0].xMin, atlasUVs[0].yMax);
UVs[20] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMin);
UVs[21] = new Vector2(atlasUVs[0].xMax, atlasUVs[0].yMax);

mesh.uv = UVs;
return model;
}