You wouldn't get the prompt because the distribution code told TurboTax that you removed the excess. The excess funds that were withdrawn will be listed on Form 1099-SA as a distribution, in Box 1, for the tax year in which the distribution was taken. Earnings on excess contributions withdrawn will be in Box 2 and included in Box 1.
To verify you are not penalized for that entry, look for Form 5329 in your return. If you were penalized, the penalty would show up on Line 8 of Schedule 2.
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