List is created correctly in Start() but returns size 0 in play mode

Try Moving assignment of the list "Matrix" to the Awake() method instead of Start() cause it looks like you call your list before Start() method in HexID class has done the assignment

Thanks for reply; I used Awake with no results; looks like that by adding

  void Update() { if (Input.GetKeyDown(KeyCode.A)) GetListCount(); }
  public void GetListCount() { Debug.Log("Matrix size is " + Matrix.Count); }

the returned value is correct, but I can't manage to call GetListCount() from another class.

I have been trying to restructure my code, but the problem persists.. Right now, I have class HexGrid attached to a GameObject, in additon to create the Matrix the script arrenges a prefab into a Hexagonal Grid. I have attached to this prefab a Controller Class that calls the size of the matrix onMouseDown.. but it keeps returning zero.

is there maybe something wrong with my hierarchy? I am posting the whole code to provide as many info as possible. Thanks all for helping. I have arranged the code that creates the matrix into another class file =>

 using System.Collections.Generic;
 namespace Pasquale.CSharp {

 public class MatrixData
 {

     public List<HexID> Data= new List<HexID>();;

     public class HexID
     {
         public int ID { get; set; }
         public string Name { get; set; }
         public int X { get; set; }
         public int Y { get; set; }
         public bool Active { get; set; }
     }

     public MatrixData(int gridSizeX, int gridSizeY)
     {
          
         int ID = 0;
         for (int y = 0; y < gridSizeY; y++)
         {
             for (int x = 0; x < gridSizeX; x++)
             {
                 Data.Add(new HexID() { ID = ID, Name = "(" + x + ", " + y + ")", X = x, Y = y, Active = false });
                 ID++;
             }
         }
     }
 }
 }

== HexGrid Is Attached to an Empty GameObject and a sprite prefab (a hexagonal tile) is attached to HexGrid ===

 using System.Collections.Generic;
 using UnityEngine;
 using System.Linq;
 using Pasquale.CSharp;

 public class HexGrid : MonoBehaviour {
   
 public int gridSizeX;
 public int gridSizeY;
 public float hexWidth;
 public float hexHeight;
 public float gap = 0;
 MatrixData Matrix;

 Vector2 startPos;
 public Transform HexPrefab;

 void Start()
 {
     AddGap();
     CalcStartPos();
     Matrix = new MatrixData(gridSizeX, gridSizeY);
     CreateGrid();
 }

 void AddGap()
 {
     hexWidth += hexWidth + gap;
     hexHeight += hexHeight + gap;
 }

 void CalcStartPos()
 {
     float offset = 0;
     if (gridSizeY / 2 % 2 != 0)
         offset = hexWidth / 2;
     float x = -hexWidth * (gridSizeX / 2) - offset;
     float y = hexHeight * 3 / 4 * (gridSizeY / 2);
     startPos = new Vector2(x,y);
 }

 Vector2 CalcWorldPos(Vector2 gridPos)
 {
     float offset = 0;
     if (gridPos.y % 2 != 0) 
         offset = hexWidth / 2;

     float x = startPos.x + gridPos.x * hexWidth + offset;
     float y = startPos.y - gridPos.y * hexHeight * 3 / 4;

     return new Vector2(x, y);
 }

 void CreateGrid()
 {
     foreach (MatrixData.HexID item in Matrix.Data)
     {
         Transform hex = Instantiate(HexPrefab) as Transform;
         Vector2 gridPos = new Vector2(item.X, item.Y);
         hex.position = CalcWorldPos(gridPos);
         hex.transform.SetParent(this.transform);
         hex.name = item.Name;
     }
 }

 void Update() { if (Input.GetKeyDown(KeyCode.A)) GetListCount(); }

 public void GetListCount() { Debug.Log("Matrix size is " + Matrix.Data.Count); }

 public void SetStatus(string name, bool status) { Matrix.Data.Where(d => d.Name == name).First().Active = status; }

 public List<MatrixData.HexID> GetList() { return Matrix.Data; }

 }

======this class is attached to the hexagonal tile prefab.. I am trying to access the matrix to manipulate its data=====

 public class Controller:MonoBehaviour {

 public GameObject HexTile;
 public List<MatrixData.HexID> gridController = new List<MatrixData.HexID>();

 private void OnMouseDown()
 {
     
     Debug.Log(HexTile.name);
     Debug.Log(gridController.Count);
      
 }
 }

Thanks again!