There are two requirements for tax free Roth IRA withdrawals. It sounds like your spouse may not have owned the Roth account more than 5 years. The 1099R for the distribution shows the taxable amount in box 2a and the box 11 shows the first year of contribution.
1. Must be over age 59 1/2
2. Must have owned the Roth over 5 years.
If the taxpayer meets the age requirement, but has not owned the Roth account more than 5 years then the penalty does not apply, but they will pay taxes on the part of the withdrawal that is earnings.
If the taxpayer does not meet both of these requirements they will pay tax on the earnings withdrawal and a 10% early withdrawal penalty.
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