What is it you're saying the program did wrong?
If the $709.98 was for the penalty, that's how it works. The penalty accumulation stops on the day the IRS receives your tax payment - which is rarely the date you file your tax return. The IRS gets what you owe, penalty accumulation stops and the IRS sends you a separate bill for the penalty amount owed.
Take a look at your 1040 line 23. The amount there is just an estimate. Note that the line is titled "estimated" tax penalty, because that amount is based on the date you prepared the return - not the date you filed it or the date the IRS received it.
Now if the bill includes additional tax and that $709.98 is more than just a late payment or under payment penalty, more than likely the IRS is aware of income you failed to report on your tax return for whatever reason. In that case, that's not a program fault or error. The program can only work with the data you enter into it, and that's it.
What form letter did the IRS send you? It's at the top and starts with "CP" or "LTR". Depending on the specific letter sent, it will tell you why you owe the additional money. Some of those form letters can be rather cryptic. So if you'll share the form number, we can help you understand it if necessary.
