It's not clear what you are looking at. There is no refund amount at the top left of an amended return. Look at the actual Form 1040-X, not a screen in TurboTax. The refund from your original tax return should be on Form 1040-X line 18. The amount that you have to pay back - the difference between the original refund and the reduced refund - should be on Form 1040-X line 20. TurboTax does calculate the difference between the two refund amounts. That difference is what is on Form 1040-X line 20.
If you have further questions, please give specific form and line numbers and exact amounts. It can be hard to figure out what's going on if you give approximate or rounded amounts.
