The 1099-R you received for the over contribution needs to be entered as a 1099-R, this will have the program calculate the 10% penalty for early distribution.
The only part of your distribution that would receive the 10% penalty is the amount of earnings on the excess contribution. Since it you are removing the over contributed amount from a Roth account the amount you contributed to the Roth account is not taxable when you remove it.
@CarloP
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