Why is my direct-deposited refund or check lower than the amount in TurboTax?
If your IRS-issued tax refund comes in around $35 or $40 less than the amount shown in TurboTax, it's probably because you used the Refund Processing Service (aka "pay-with-your-refund") to pay your TurboTax fees. There is a separate processing fee for this service, which is deducted from your federal refund in addition to your TurboTax fees.
Other missing dollar amounts may be caused by a refund offset. This is when the government applies part or all of a taxpayer's refund towards the taxpayer's past-due income tax, child or spousal support, student loans, or state unemployment compensation debts.
If this happens, you should be getting a letter from the government explaining why you didn't get the entire refund. You can also get this information by looking up your refund at the IRS Where's My Refund page.
Finally, the government may have made a correction to your tax return, resulting in a lower (or higher!) than anticipated refund. Again, you'll get an official explanatory letter when this happens.