There are a couple of thing that may have happened.  It's possible that you had the Refund Processing Service, a $39.99 service that will take your TurboTax fees out of your refund.  If you forgot that you choose to pull your fees of your refund that could be a shock. 

Another option is that all or part of your refund may have been offset by the IRS.  Typically, you'll get a notice before the IRS does anything with your refund such as if they make corrections to your return or offset your refund to pay off past due taxes, child support, etc.