No, The IRS will compute any penalty fees once they process the return.

https://ttlc.intuit.com/replies/4843152

Even with the Healthcare penalty? I answered all the questions and I got a message that said I was waived of the Healthcare penalty.. I didn't have health care for 5 months due to the high cost of insurance and me being unemployed for those 5 months.. Is the message correct or will I get another message from the irs saying I have to pay?

With the health care penalty the program in some cases will let you know if the penalty is waived. So if you were waived then you are good to go. <a rel="nofollow" target="_blank" href="https://ttlc.intuit.com/replies/4843152">https://ttlc.intuit.com/replies/4843152</a>

So as long as I got that message after I answered the questions then my tax return should be approved by the irs right?

Yes.