box 12W indicates you had employer contributions (under the tax laws both your contributions and any matching employer contributions are reported as employer contributions) to a HSA account. that requires filing form 8889. you also need to report that you spent the entire account on qualified medical expenses. you should have gotten a 1099-SA for that. the $3,000 should only appear on line 9 and not line 2 of the form. so your choice is to amend now or wait for an IRS notice which is sure to come sooner or later. the HSA trustee sends reports of contributions and distributions to the IRS so when it goes to match it will find missing info which will delay any refund depending on the timing of your return submission and the trustee sending the reports to the IRS. if that 12W is not right then you have to contact your employer to have it corrected. 12DD is irrelevant and does not affect your taxes
