This most likely occurs because you made uneven estimated tax payments.
1/4 of any withholding is assumed to have been paid for each period ending 3/31, 5/31, 8/31, and 12/31
estimates are only credited for the period paid. the default is that 1/4 of your income tax is due each period (estimates by the 15 of the month following). Thus uneven estimates can result in penalties because of the default method.
You can use the annualized income installment method on page 3 of the 2210 to see if that will lower your penalties.
