Employer left Box 12 - W blank, so I counted the HSA contributions as my contributions. Now Employer gave amended W-2 with Box 12 W and I owe extra taxes. Why??

In the amendment, I added Box 12 -W, and deleted the figure I had added under my own contributions (I put it there because there was nothing in Box 12 on my original W-2). Why do I now owe taxes on my contribution amount?