c# List not fully clearing

Is there any reason a List won't fully empty despite being given specific commands? I have an if statement which reads:

if (myTransform.position.y <= -12.8f)

     {
         //ballState = BallState.RestingBall;
         GameManager.CalculateScore(ballColor);
         //create a popper in the lane where it went through
         Instantiate(Popper, new Vector3(myTransform.position.x, -10f, myTransform.position.z), Quaternion.identity);
         Instantiate(PopperBloom, new Vector3(myTransform.position.x, -10f, myTransform.position.z), Quaternion.identity);

         BallList.Remove(this);
         Destroy(gameObject);

     }

I'm finding that it works for various balls going off the bottom of the screen but for some reason the List count won't go below 1, even though all the balls disappear from the hierarchy panel in Unity. I'm keeping track of the number of balls with a simple GameManager.numBallsInList = BallList.Count; statement at the top of my Ball.Update() method. Is there a c#/Unity reason for this happening or is it me doing something wrong?