Unity Loadscene link errors

I am working on a mobile game, and am experiencing a strange bug/error. When I load into the main scene , all is fine everything works and no errors. However there are two scenario's in which it breaks

• when I open the pause menu and go to the main menu. Then return to the level all is broken.
• coming directly from the main menu into the level

GameObject links in scripts are missing and some other stuff. Here are the errors and corresponding code that is used:

If some screen from the editor are required I will update the question

Code used for the pause menu:

 public class Pause : MonoBehaviour {

    [SerializeField]private bool _isPaused;
    [SerializeField] private GameObject _attackButton;
    [SerializeField] private GameObject _moveButton;
    [SerializeField] private GameObject _pauseMenu;
    [SerializeField] private GameObject _pauseButton;

    // Use this for initialization
    void Start () {
        _isPaused = false;
        _pauseMenu.SetActive(false);
    }

    // Update is called once per frame
    void Update () {

    }

    public void OnClickPauseButton()
    {
        _isPaused = !_isPaused;
        if(_isPaused)
        {
            Time.timeScale = 0;
            HideButtons();
        }
    }

    public void OnClickResumeButton()
    {
        _isPaused = !_isPaused;
        if (!_isPaused)
        {
            Time.timeScale = 1;
            ShowButtons();
        }
    }

    public void OnClickMenuButton()
    {
        SceneManager.LoadScene("MainMenu");
    }

    private void HideButtons()
    {
        _attackButton.SetActive(false);
        _moveButton.SetActive(false);
        _pauseButton.SetActive(false);
        _pauseMenu.SetActive(true);
    }

    private void ShowButtons()
    {
        _attackButton.SetActive(true);
        _moveButton.SetActive(true);
        _pauseButton.SetActive(true);
        _pauseMenu.SetActive(false);
    }
}

The Main menu code, that is used

 public void StartGame()
 {
        SceneManager.LoadScene("2DScene");
 }

 public void ClickUnfinishedButton()
 {
        StartCoroutine("FadeInAndOutText");
 }

 IEnumerator FadeInAndOutText()
 {
        toBeAddedText.SetActive(true);
        yield return new WaitForSeconds(2);
        toBeAddedText.SetActive(false);
}

EDIT:

Scoremanager code:

public class ScoreManager : MonoBehaviour {

[SerializeField] private PlayerController _player;
[SerializeField] private GameObject text;
[SerializeField] private Slider SliderVar;
private int _currentScore, _requiredScore;

// Use this for initialization
void Start()
{
    InitializeVariables();


}

private void InitializeVariables()
{
    _player = _player.GetComponent<PlayerController>();
    _requiredScore = 10;
}

// Update is called once per frame
void Update()
{
    setScoreSlider();
    text.GetComponent<Text>().text = _player._currentScore + "/" + _requiredScore;
}



private void setScoreSlider()
{
    SliderVar.value = _player._currentScore / _requiredScore;
}
}

Code from inputscript:

 public class InputScript : MonoBehaviour
{
    public FingersJoystickScript joystickScript;
    [SerializeField] private float _minimumDistanceSwipe;
    [SerializeField] private float _minimumSpeedSwipe;
    [SerializeField] private SwipeGestureRecognizerDirection _swipeDirection;
    public GameObject player;
    public bool isAttacking;
    private TapGestureRecognizer _pressGestureRecognizer;
    private Vector2 _smoothDirection;
    private SwipeGestureRecognizer _swipeGestureRecognizer;
    private LongPressGestureRecognizer _longPressGestureRecognizer;
    private bool _facingRight = false;
    private Animator anim;



    private GestureTouch FirstTouch(ICollection<GestureTouch> touches)
    {
        foreach (var t in touches)
        {
            return t;
        }
        return new GestureTouch();
    }

    private void Awake()
    {
        joystickScript.JoystickExecuted = JoystickExecuted;
        joystickScript.MoveJoystickToGestureStartLocation = false; 
        isAttacking = false;
    }

    //  public bool MoveJoysticktoGestureStartLocation;

    private void Start()
    {
        anim = player.GetComponent<Animator>();
        CreateSwipeGesture();

        _swipeGestureRecognizer.MinimumDistanceUnits = _minimumDistanceSwipe;
        _swipeGestureRecognizer.MinimumSpeedUnits = _minimumSpeedSwipe;
        _swipeGestureRecognizer.Direction = _swipeDirection;
    }

    private void Update()
    {
        _swipeGestureRecognizer.MinimumDistanceUnits = _minimumDistanceSwipe;
        _swipeGestureRecognizer.MinimumSpeedUnits = _minimumSpeedSwipe;
        _swipeGestureRecognizer.Direction = _swipeDirection;


    }

    private void CreateSwipeGesture()
    {
        _swipeGestureRecognizer = new SwipeGestureRecognizer
        {
            Direction = SwipeGestureRecognizerDirection.Any,
            DirectionThreshold = 1.0f
        };
        _swipeGestureRecognizer.Updated += SwipeGestureCallback;
        FingersScript.Instance.AddGesture(_swipeGestureRecognizer);
    }

    private void SwipeGestureCallback(GestureRecognizer gesture, ICollection<GestureTouch> touches)
    {
        if (gesture.State == GestureRecognizerState.Ended)
        {
            isAttacking = true;
        }

    }

    private void JoystickExecuted(FingersJoystickScript script, Vector2 amount)
    {
        if (amount.x > 0 && !_facingRight)
        {
            FlipXAxis();
        }
        else if (amount.x < 0 && _facingRight)
        {
            FlipXAxis();
        }
        Vector3 pos = player.transform.position;
        pos.x += (amount.x * 8 * Time.deltaTime);
        pos.z += (amount.y * 8 * Time.deltaTime);
        player.transform.position = pos;
        anim.SetBool("isWalking", true);

        if (amount == Vector2.zero)
        {
            anim.SetBool("isWalking", false);
        }
    }

    private void FlipXAxis()
    {
        //oposite direction
        _facingRight = !_facingRight;

        //get local scale
        var theScale = player.transform.localScale;

        //flip on x axis
        theScale.x *= -1;

        //apply that to the local scale
        player.transform.localScale = theScale;
    }

}