Get your taxes done using TurboTax

It sounds like you entered the same tax payments in 2 areas of the program which resulted in the tax payments being reported twice in your return.  

The MCTMT payments should have been entered in the state interview section of the program.  

1. In this state section, you would need to proceed through the screens until you get to the screen titled "take a look at New York credits and taxes."
2. On this page, you need to scroll down to the section titled New York City and Metro Commuted Taxes.
3. Then, select edit/start to the right of Metro Commuter Transportation District Self-Employment Income.
4. Proceed through the screens until you see the page allowing you to enter the dates of the payments and the amounts paid as shown in the sample page below.

If you entered the payments anywhere else with TurboTax, you should consider amending the return to make the correction.  However, if the taxing agency has already sent you a letter informing you of the error, then you can simply follow the instructions in the letter to remedy the error.