I had a refund once and still had a penalty for not paying in evenly during the year. You can leave the penalty line blank and let the IRS figure any penalty due. When you went though the underpayment section form 2210 did you fill out all the quarterly amounts for income and withholding, etc?
If you are filling out form 2210 Schedule AI then watch out for the dates. They are different than quarterly dates. And all start with Jan 1. You will need to add up the individual paychecks and income.
If you file with a penalty or without the penalty, it's common and normal and expected for the IRS or state to bill you for more or send you a refund.
