There are a few reasons why your deposited refund would not be the total shown. The first would be if you used the Refund Processing Service, which is where you pay your TurboTax fees from your Federal Refund. Another reason could be an Offset.
A refund offset is when an IRS refund is reduced or intercepted to pay off delinquent debt, such as past-due child support, outstanding student loans, or unpaid state income tax. You'll get an explanatory letter from the Bureau of the Fiscal Service if your refund is offset. The remainder of your refund will be processed as usual; an offset shouldn't delay it, unless of course your entire refund was applied to your debt.
In order to be certain, you can also contact the IRS directly to determine the cause for a lowered refund amount. You can do so by clicking the link below and selecting the office nearest you:
https://www.irs.gov/uac/Contact-Your-Local-IRS-Office-1