you need to make sure the gameobject window that you instantiate also has a collider and you will call your OnMouseDown() from the window script.

It looks like the overlapping is causing your issue since the collider will be already colliding with the window. You can solve this problem a couple ways. you can create a new layer and set the window object to that layer. then in physics 2d settings you can set the collision matrix to not collide with each other. Or you can possibly set the windows z position to be in a spot that wont collide.

you are asking if hasWindow when there is no window so the instantiate is not firing properly. you can either change it to hasBeenTouched or set the hasWindow bool to true in the OnMouseDown for it to fire.

 if (hasBeenTouched)
    {

        if (window == null)
        {
            window = (GameObject)Instantiate(Resources.Load("Prefabs/OtherPrefabs/Window"),
                new Vector3(transform.position.x + 0.5f * gameObject.GetComponent<SpriteRenderer>().bounds.size.x, transform.position.y + 0.5f * gameObject.GetComponent<SpriteRenderer>().bounds.size.y, transform.position.z),
                Quaternion.identity);
            window.name = gameObject.name + "Window";
        }
    }

you need to make sure the gameobject window that you instantiate also has a collider and you will call your OnMouseDown() from the window script.