OnMouseDown() and Collision not working for game object created within another game objects script

I have created a game object (Brick) and added a script (BrickScript) to it. Within this script I create a Window game object if a certain condition is satisfied. Please see code below:

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

The Brick and window game objects actually overlap a bit. I realized that when hasWindow = true (the window is created) the condition in the code below is not satisfied and other game objects don't collide with the Brick. But when hasWindow = false (the window is not created), everything seems to work well. How can I solve this?

void OnMouseDown () {
    if (Input.GetMouseButtonDown(0)) {
        Debug.Log ("touch down");
        hasBeenTouched = true;
    }
}