There are many reasons why your refund could be less than what was calculated after it was received and processed by the IRS. If the IRS sees that you have any unpaid taxes, student loans, child-support, etc. then they can seize part or all of your refund to cover the cost of what is owed. TurboTax has no access to a tax filer's unpaid debts. Also, if there was any information that was input incorrectly on your return then verified by W2s or 1099s that the IRS receives along with you then they will adjust the return to reflect the correct amount of federal withholdings, wages & income, social security paid, etc. Your employer is required to send you and the IRS a copy of your W2 or 1099 if you are an independent contractor. Also, if you chose to have your tax preparation fees deducted out of your refund versus paying for them upfront then of course you would receive the difference of what that amount is. When you elect to have your tax preparation fees deducted from your tax return there is a fee for doing this called a Refund Processing Fee of $34.99. Here is additional information about refund offsets.
You can also call the IRS at 1-800-829-1040 and speak to a representative that may be able to give further detail into why your refund from the IRS was different from what you calculated in TurboTax's software.
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