TurboTax does not get any information from the IRS or your state after you file your tax return. You say you received a "letter" but you do not say who it was from or what it said. Was your refund offset for a debt you owed--like child support or back taxes? We can only guess why your refund was less than you expected unless you say what the letter told you.
There can be a number of reasons why your refund was less than the amount you expected. First of all, look carefully at your actual tax returns. There is sometimes confusion about the amount of refund to expect when users misinterpret the “summary” they saw in TurboTax. The amount of your refund is on your tax return.
TurboTax does not receive feedback from the IRS regarding money that was offset from your refund. If you owed back taxes, child support, student loan debt, etc. you will receive a letter of explanation from the IRS in several weeks. The WMR site will contain a message regarding your offset. It is also possible that the IRS caught a mistake you made and reduced your refund.
It is also possible that your state reduced your refund for debts owed in your state—if the state reduced your state refund you will receive a letter from the state.
IRS Treasury Offset Program Call Center at 1-800-304-3107
Be aware also that your Federal refund and state refund do NOT come together. Federal and state tax returns are processed by two completely separate entities.
Did you choose to have TT fees deducted from your Federal refund? (Remember that if you did that, you also agreed to an extra refund processing fee of $39.99)
How can I see my TurboTax fees?
To see back taxes owed
NOTE: You can contact the IRS Treasury Offset Program Call Center at 1-800-304-3107 to ask if they have an offset for you on file. TurboTax would not have that information.
Or did the letter request something from you--such as a request to verify your identity?