My federal tax refund in turbotax and IRS is 'x'.I received 'y' to my checking account and price for turbotax services was 'z'. Sum of 'y' an 'z' is less than 'x' by 40$.

Only the ones that you agreed to prior to filing.

If you've chosen to have the TurboTax preparation fees deducted from your federal refund, you will incur a Refund Processing Fee of $39.99 (in addition to the preparation fees).  This was explained on the screen where you chose to pay by refund or pay by credit card. And had to be agreed to on the screen following.

You can avoid that additional fee, by paying the TurboTax preparation fee up front using a credit or debit card.

If you haven't filed yet, you can remove that fee by following the instructions here:
https://ttlc.intuit.com/questions/1900517-how-do-i-remove-the-refund-processing-service

Thank you!