其实你不需要一面旗子。
你的战斗结果是完全对称的，这意味着任何一方是赢家。
因此，在我看来，最简单的解决办法是只让获胜（或交替失败）的一方处理战斗的结果，并做例如。

// Note that your tag check is actually redundant
// this would already be enough and you don't need to remember assigning tags
if(collision.gameObject.TryGetComponent<ShipBehaviour>(out var shipBehaviour))
{             
    if(shipBehaviour.ShipsInside < ShipsInside)
    {
        ShipsInside -= shipBehaviour.ShipsInside;
        Destroy(shipBehaviour.gameObject);
    }
    else if (shipBehaviour.ShipsInside == ShipsInside)
    {
        Destroy(shipBehaviour.gameObject);
    }
}

这应该足够了，因为另一个冲突方已经处理了他们这边的其他情况。
当然，你也可以反过来处理你自己的失败案例。同样的，你可能更喜欢在==案例中只毁灭自己。
如果你不关心这个多余的减法（因为物体无论如何都会被破坏），你甚至可以把它缩短为

if(collision.gameObject.TryGetComponent<ShipBehaviour>(out var shipBehaviour))
{             
    if(shipBehaviour.ShipsInside <= ShipsInside)
    {
        ShipsInside -= shipBehaviour.ShipsInside;
        Destroy(shipBehaviour.gameObject);
    }
}

您只需添加一个标志即可解决此问题。

private bool _collisionHandled = false;

private void OnCollisionEnter(Collision collision)
{
    if (_collisionHandled || collision.gameObject.tag != "Ship")
    {
        return;
    }

    var shipBehaviour = collision.gameObject.GetComponent<ShipBehaviour>();
    if (shipBehaviour != null)
    {
        if (shipBehaviour.ShipsInside > ShipsInside)
        {
            shipBehaviour._collisionHandled = true;
            shipBehaviour.ShipsInside -= ShipsInside;
            Destroy(gameObject);
        }
        else if (shipBehaviour.ShipsInside < ShipsInside)
        {
            _collisionHandled = true;
            ShipsInside -= shipBehaviour.ShipsInside;
            Destroy(shipBehaviour.gameObject);
        }
        else if (shipBehaviour.ShipsInside == ShipsInside)
        {
            _collisionHandled = true;
            shipBehaviour._collisionHandled = true;
            Destroy(gameObject);
            Destroy(shipBehaviour.gameObject);
        }
    }
}