Your and your employer's contributions count as one as far as the total is concerned. So when TurboTax is calculating and excess (plus any earnings) that is the amount of contributions that needs to be removed to avoid the penalty. No distinction between employee and employer contribution is necessary. Just remove the excess amount as calculated.
The earnings portion is not calculated by TurboTax. It is up to the taxpayer to request the withdrawal of any earnings when making the excess contribution withdrawal from their fiduciary.
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