If proper estimated tax payments were not made does Turbo tax compute the penalty when filing or do you wait for the IRS to take exception?

The program will compute an estimated underpayment penalty and add it to your return ... however the IRS reserves the right to adjust that amount and add a failure to pay, failure to file and interest based on when you actually file & pay the balance due.   Same with any state returns. 

<a rel="nofollow" target="_blank" href="https://www.irs.gov/businesses/small-businesses-self-employed/understanding-penalties-and-interest">https://www.irs.gov/businesses/small-businesses-self-employed/understanding-penalties-and-interest</a>