The obvious answer maybe that the calculator is kind of imperfect , so use it as a tool to guess more or less but dont trust it 100%

However if you really want to calculate it , there is a much powerful tool available its ..... your brain

Find the distance flown on flightradar then use the charts to get the value

Before buying , ask on forums , FB and maybe CI if anyone had collected miles according to the accrual scheme and if there wasnt any trap