There's been no systematic issue reported for the TTX software over-reporting withholding or estimated taxes paid. 99.9% of all errors result from users double-reporting certain withholding (or estimated taxes) tax pre-payments.
Possibilities or instances from past years that I can think of, where the user over-reported tax withholding, or estimated tax prepayments:
1) Employee Stock option exercises: They get a 1099-B/8949 from the brokerage and the user accidently indicates that a certain amount of the gains was applied to tax withholding.....nope....not there ! The gains are reported, and extra withholding is already showing and reported on the W-2 they received from their employer....it isn't to be reported again on the brokerage 1099-B/8949 entries.....it's on the W-2 !. TTX can't know you double-reported.
2) Double-reporting W-2, or 1099-R tax withholding (or other forms with withholding already shown & entered): You enter your W-2 or 1099-R (or other tax form, like an SSA1099 , W-2G, some1099-G's ) once on the Income page with all it's boxes. There is a second area on the Deductions& Credits page where a user can enter any tax withholding Not Already Reported elsewhere. A few people have absent-mindedly double-entered their W-2 or 1099-R withholding again there. TTX can't know you double-reported.
3) Quarterly Estimated Tax Payments: Occasionally someone enters more quarters of Estimated tax payments than they actually payed. TTX can't know you entered more estimated payments than you actually made.
4) Refunds from one year rolled over to the next year: A user enters the refund rollover into the tax software .... both as a refund rolled from the last year to the current year, and a second time as a 1st Qtr Estimated tax payment. TTX can't know you double-reported.
5) ??? Simple fumble-fingered keystroke errors: TTX can't know that.
And if you claimed excess Social Security withholding. Are you married? If you filed a joint return and both spouses have W2s you have to enter each W2 under the right name or it will look like all the W2s belong to only 1 person and too much social security tax was paid for that 1 person. And by assigning both W2s to the same person the program wouldn't know a W2 is missing from the spouse. It just would think they are both for you.
What year? I would check over your return and see if you can see anything wrong especially in the payments section 1040 lines 17 & 18. Make sure you agree with all the amounts listed. Like is the difference the same or close to the refund you got last year? Maybe you put down that you applied last year's refund to this year? Or you put down you made a payment with an extension or paid an estimated payment that you didn't make?
6) A year you filed an extension? : And maybe didn't pay the indicated extension amount....but left it in as having being paid with the extension when you actually filed your final tax forms. That's one that we've seen more than a few times.