The penalty on line 38 is included in line 37 or reduced a refund on line 35a. Nothing you can do about it now. The IRS may recalculate it and send you a bill for more or send you a refund. If you had noticed before you filed we could have told you how to try to eliminate or reduce it.
It's not for filing or paying late. It doesn't have to do with last year's tax return or not paying estimates for this year. The penalty is an "estimated" amount. It's a penalty if you owe too much or for not paying in enough withholding during the year or not paying in evenly. Even if you are getting a refund you can still owe a penalty.
