I received a direct deposit of $628 my refund is $2694. I owed state 1700. The state took my refund of $376 which would leave my total owed at $1314.

[corsawc410]

This would give me a total of 1380. Subtract the 39.99 I was made to pay TurboTax to file. Leave me with 1340 left where is the rest.

[MonikaK1]

Different agencies process your federal and state refunds, so the two need to be considered separately. 

If you elected to pay your TurboTax fee from your refund, that would have come from your Federal refund. In addition, the bank that processes the TurboTax fee also charges a fee of $39, so that charge would be in addition to the cost of your TurboTax products. 

If you owed Federal taxes from another tax period, the IRS could also have taken funds from your refund to cover those taxes owed. In addition, if you owe amounts to another Federal agency, such as a defaulted student loan, the IRS can apply part of your tax refund to pay those debts.

See this help article, Why is my refund direct-deposit or check lower than the amount in TurboTax? for more information on this topic.

[Critter-3]

Did you check the IRS for the amount they paid out after the state balance due?  It is possible that the state balance due was taken from the federal refund AND they also withheld the state refund ... so if the state gets overpaid they should eventually refund you the excess after any penalties/interest/fees are covered.

And take a look at the TT fees ... the Deluxe version was $39  +  the state (if you had one) $39  + the processing fee of $39 to have the TT fees withheld from your federal refund ... it was not just $39.   AND you did not have to use the refund processing service if you just paid the TT fees upfront with a CC. 

How to see your fees
https://ttlc.intuit.com/questions/2565973-how-do-i-review-my-fees-in-turbotax-online   

[CatinaT1]

The IRS and State Governments have the ability to offset a refund to pay for certain past due debts.  You generally will receive a letter stating what the offset was for.   

The IRS provides a toll-free number, (800) 304-3107, to call for information about tax offsets.