In general, to avoid an estimated tax penalty you would want to meet the Safe Harbor requirements (See: Underpayment of estimated tax by individuals penalty )
- Pay at least 90% of your current year's tax liability: Estimate your total tax liability for the current year and ensure your payments (withholding and estimated payments combined) cover at least 90% of that amount.
- Pay 100% of your previous year's tax liability: You can avoid a penalty by paying 100% of the tax shown on your previous year's return (110% if your adjusted gross income was over $150,000, or $75,000 if married filing separately).
Based upon you receiving a CP-30 you did not meet the Safe Harbor requirements.
The $1,000 threshold in estimated tax payments refers to the amount of tax you expect to owe for the current tax year, after subtracting your withholdings and refundable credits. Your estimated tax payments that you made for all four quarters are not included in this calculation. In short, since the refund was generated because of the estimated tax payments and not withholding and refundable credits this is the reason you have an estimated tax penalty.
The next two questions are intertwined. While TurboTax automatically calculates and adds an underpayment penalty to your tax return if you didn't pay enough estimated taxes throughout the year, or if your withholding wasn't sufficient, it would appear your preparer did not do so. I would say it is best to calculate the penalty, as Turbo Tax does, as well as annualize income if there was income that was received during the year that is not equal across the quarters.
Thank you for your question @Dan S9
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Marc T.
TurboTax Live Tax Expert
28 Years of Experience Helping Clients
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