A Roth account with funds in there 5 years or more means there is no tax for removing your own contribution amount, but that is determined relative to Basis and Account Balance and the sequence of the distribution(s). Code J introduces the 10% early withdrawal penalty, unless an exception applies.

Have you entered the Basis? The Account Balance? The program needs all of this info to do the math.

Did you work through the Fed step-by-step as I provided already:

https://www.irs.gov/help/ita/is-the-distribution-from-my-roth-account-taxable

Then, confirm that same info for MA at the link I provided.

Otherwise, I'm not sure what you still are asking about. Sorry.

"subtracted her Roth Contributions"

If the distribution exceeds the basis in the account, then she took her own money and some earnings. The Earnings would be taxable. Or, the distribution does not exceed basis the prior year, but this year, what she took exceeds the remaining basis. That also means she took earnings. Earnings are taxable when you violate the regulations that would have made them not taxable.