Get your taxes done using TurboTax

Every year I pay estimated taxes so that total taxes paid are the same as the previous year. That means there should be no penalty, but Intuit added a penalty nevertheless. Is this a penalty because I didn't "register" my desktop software? I can find no way to override the error, and I cannot file a form which says the software added the amount incorrectly. Why do I have to fight against tax prep software to get my taxes correct? Can I get a refund for the fact that I am no longer allowed to eFile if I correct the erroneous penalty?