You didn't say if the IRS figure at the IRS WMR site is more or less than TurboTax, so I'll assume the IRS site is saying you will get less than what you claimed.
First of all, be sure you don't use the total of both Federal and state refunds when comparing. TurboTax website shows a summary figure that is both refunds added together. If you're getting a state refund, it comes separately in a different deposit. So be sure you are using only the Federal refund amount for comparison with the IRS site. Look at your Form 1040, Line 35a.
Also, if you are paying any product fees out of your Federal refund, be sure you account for those, plus an additional $40 service fee for that option ($45) for California filers.
Otherwise, if the IRS did change the amount (i.e., different than Line 35a), then watch for a letter that will explain why it was changed. Also see this FAQ for possible reasons:
FAQ: Why is my refund direct-deposit or check lower than the amount in TurboTax?
If you need info before receiving your letter, you can phone the IRS or if due to an offset, the Bureau of the Fiscal Service.