It is not right but many organisation has deduct TDS on total amount of invoice/bill and some on without service tax.
But
there is logic, it is that the organisation (who made the payment) is not consider with the amount of service tax because they pay total amount and the rule is, you calculate TDS on the amount which you pay.
For the organisation the payment is of total amount so they deduct on it.
There is only remedy in that case that we should not charge service tax when our income is not more than Rs.10,00,000/-
OK