Did you have a penalty on 1040 line 38? Even if you don't the IRS can assess you a penalty. It has nothing to do with paying or not paying the tax due or quarterly estimates. The penalty is an "estimated" amount.
If you do not pay in enough tax from withholding and estimates, you may have to pay a penalty for underpayment of estimated tax. Even if you are getting a refund you can still owe a penalty for not paying in evenly during the year. Generally, most taxpayers will avoid this penalty if they owe less than $1,000 in tax after subtracting their withholdings and credits, or if they paid at least 90% of the tax for the current year, or 100% of the tax shown on the return for the prior year, whichever is smaller. It is included in your tax due or reduces your refund.
