One possibility is you used the Refund Processing Service to pay your TurboTax Online fees. If you did, your TurboTax fee plus the additional processing fee is deducted from your federal tax refund.
Another possibility is your refund was reduced by the government, either to correct a calculation error or through a refund offset.
The IRS Where's My Refund tool will contain a disclaimer if your refund may have been offset. You'll get an explanatory letter from the government if your refund differs from what was on your filed return.
Were you getting a refund from both federal and state? They may have been sent at different times by the IRS and state.