My federal return is $1,292, TT fees are $147, but TT only deposited $1,104.01, short $40.99. TT claims they “accidentally” overcharged $36.25. Math doesn’t add up?

Did you have the income tax credit? 

We’re aware of an issue related to your Refund Processing that may have caused you to see a smaller-than-expected refund.
We’re in the process of reimbursing all who were affected. Within the next 24-48 hours, those affected will receive a credit. If you were affected, look for a deposit (in the bank account associated with your return) labeled, “Remaining Federal Refund Due.  If you don't see that deposit in a few business days, please reach out to us directly using the Help Article here.