If you are saying that you completely finished your return and the program said what your federal refund was but when you received the direct deposit or refund check, it was for a different amount, that probably means the taxing agency (IRS in this case) offset your refund for a something on the tax return that was missing, a past due income tax, child support, student loans, or some other obligation.
You should receive a letter from the government entity, explaining why you didn't get the refund.
If this happened with your Federal Refund you can also get that information by checking the Where's My Refund page on IRS.gov. Here is a link to that page: Where's my Refund?
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