If you were to receive both a federal tax refund and a state tax refund, those refunds are sent separately by separate tax authorities.
If you requested to have the TurboTax account fees paid from the federal tax refund, the federal refund received will have those fees deducted along with the $40 service charge for that option.
For federal tax refund FAQ's go to this IRS website - https://www.irs.gov/refunds/tax-season-refund-frequently-asked-questions
Why is my refund different than the amount on the tax return I filed?
All or part of your refund may have been used (offset) to pay off past-due federal tax, state income tax, state unemployment compensation debts, child support, spousal support, or other federal nontax debts, such as student loans. To find out if you may have an offset or if you have questions about an offset, contact the agency to which you owe the debt.
We also may have changed your refund amount because we made changes to your tax return. You’ll get a notice explaining the changes. Where’s My Refund? will reflect the reasons for the refund offset when it relates to a change in your tax return.
Tax Topic 203 - Refund Offsets for Unpaid Child Support, Certain Federal and State Debts, and Unempl... has more information about refund offsets.
Exactly $250? That could be the amount of the first time home buyer credit repayment. Did you claim that credit in 2008 and possibly owe repayment now?