Re-loading a scene but on the background older scenes are displayed

Hello there. I was testing my game, when I noticed a strange thing: when I do game over by making the time expires, loading again the same scene displays on the background the older scenes that I completed precedently.

Here's an example: this pitcure represents the beginning of the second level. Notice the timer, in the bottom right corner. I let the time expires. Then, as it is expected, it appears this canvas:

When I click on "Yes", instead of loading again the same scene, it appears this:

Which is the level completed previously!!! Clicking "yes" another time makes the scene to be loaded again.

I want to avoid this strange behavior, making the scene to be loaded again without display any older scene! This is the code which I use to manage the canvas and the buttons:

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 using UnityEngine.SceneManagement;
 using UnityEngine.UI;
 
 public class MenuScript : MonoBehaviour {
 
     public bool GameIsEnded = false;
     public GameObject mainCanvas;
     public GameObject[] weapons;
     private Text theText = null;
     public Button [] butts;
     private Scene scene;
     private int sceneIndex;
 
     void Start () {
         scene = SceneManager.GetActiveScene ();
         SceneManager.SetActiveScene (scene);
         sceneIndex = scene.buildIndex;
         theText = mainCanvas.GetComponentInChildren<Text> ();
         butts = mainCanvas.GetComponentsInChildren<Button> ();
         Debug.Log (SceneManager.sceneCountInBuildSettings);
         weapons = GameObject.FindGameObjectsWithTag ("WeaponSpawn");
     }
         
     //Update is called once per frame
         void Update () {
 
         // Handling menu for ENEMY mode
         if (Maze.genState == "Enemy" | Maze.genState == "Traps" | Maze.genState == "EnemyTraps") {
             if (CheckBehavior.verify == true && GameIsEnded == false) {
                 for (int i = 0; i < weapons.Length; i++) {
                     weapons [i].SetActive (false);
                 }
                 Time.timeScale = 0;
                 GameIsEnded = true;
                 theText.text = "You win!\nContinue?";
                 butts[0].onClick.AddListener (Continue);
                 mainCanvas.SetActive (true);
             }
 
             if (PlayerController.dead == true && GameIsEnded == false) {
                 for (int i = 0; i < weapons.Length; i++) {
                     weapons [i].SetActive (false);
                 }
                 Debug.Log ("You're dead!");
                 Time.timeScale = 0;
                 GameIsEnded = true;
                 theText.text = "You're dead!\nTry again?";
                 butts[0].onClick.AddListener (Play);
                 mainCanvas.SetActive (true);
             }
 
         }
             
         if (Maze.genState == "Timer") {
 
             if(CheckBehavior.verify == false && Timer.timeLeft <= 0 && GameIsEnded == false){
                 for (int i = 0; i < weapons.Length; i++) {
                     weapons [i].SetActive (false);
                 }
                 Time.timeScale = 0;
                 GameIsEnded = true;
                 theText.text = "Time's up!\nTry Again?";
                 butts[0].onClick.AddListener (Play);
                 mainCanvas.SetActive(true);
             }
 
             if(CheckBehavior.verify == true && Timer.timeLeft > 0 && GameIsEnded == false){
                 for (int i = 0; i < weapons.Length; i++) {
                     weapons [i].SetActive (false);
                 }
                 Time.timeScale = 0;
                 GameIsEnded = true;
                 theText.text = "You Win!\nContinue?";
                 butts[0].onClick.AddListener (Continue);
                 mainCanvas.SetActive(true);
             }
 
         }
     }
 
     
 
     public void Play () {
         mainCanvas.SetActive(false);
         Time.timeScale = 1f;
         GameIsEnded = false;
         CheckBehavior.verify = false;
         PlayerController.dead = false;
         SceneManager.UnloadSceneAsync (sceneIndex);
         SceneManager.LoadScene(sceneIndex, LoadSceneMode.Single);
         Debug.Log ("Play pressed!");
 
     }
 
     public void Continue () {
         if (scene.buildIndex != SceneManager.sceneCountInBuildSettings) {
             mainCanvas.SetActive (false);
             Time.timeScale = 1f;
             GameIsEnded = false;
             CheckBehavior.verify = false;
             SceneManager.UnloadSceneAsync (sceneIndex);
             SceneManager.LoadScene (sceneIndex + 1, LoadSceneMode.Single);
             Debug.Log ("Continue!");
         } else {
             theText.text = "Demo ended!";
             for (int i = 0; i < butts.Length; i++) {
                 butts [i].gameObject.SetActive (false);
             }
         }
 
     }
     public void QuitGame() {
         Debug.Log ("Quitting game...");
         Application.Quit ();
     }
 
 }

EDIT: I discovered that the maze displayed on the background... it's the newly reloaded scene! All my levels are procedurally generated: it seems that SceneManager.LoadScene doesn't load in time respect to the maze generation method, which "arrives" first.

EDIT: Ok, it's clear that when a game over is performed, the script I wrote enter 2 times in the "Timer" condition, adding two times the SceneLoad method to the button Yes...