My guess is that the system is telling you that you need Schedule 3 for something you entered, but it has not yet created Schedule 3 in your tax return because you are using Free Edition, which cannot produce Schedule 3. I assume it is telling you that you have to upgrade to a higher edition (which is not free) because you need Schedule 3. After you upgrade the amounts from Schedule 3 will flow to Form 1040.
I don't understand what "box 12" you are looking at. Do you mean box 12 on your W-2? Line 12 on Form 1040 has nothing to do with Schedule 3. The totals from Schedule 3 appear on Form 1040 lines 13b and 18d.
