The tax code is extremely complex, and it's impossible to answer your question with a simple one liner. All income is not taxed the same, or at the same rate. How income is taxed, depends on it's source. For example, short term capital gains are taxed differently than long term gains, which is taxed differently than W-2 income, which is taxed differently than self-employe income, and on, and on, and on.
TurboTax calculates your tax liability based on the data you enter and the answers you provide to the questions asked. If TurboTax "missed" a deduction, then most likely it's because you didn't claim it, or you answered a question or made a selection in the program that indicated to the program you did not qualify for the deduction.
If you can prove TurboTax actually made a calculation error, (this does happen a least a few times each year) then it's fairly simple to file a claim and TurboTax will pay any fines and penalties you may incur. Just understand that TurboTax will not under any circumstances pay any actual taxes you may owe as a result of a calculation error.
