If you have received a letter from the IRS, then you need to do exactly what the IRS says - amend, not amend, complete a form, provide an explanation, whatever.

In your case, my guess is that they wanted some supporting data for the HCTC. But you didn't mean to claim this credit. 

In the letter explaining that you did not intend to take that credit, ask the IRS if they will amend your return to remove that form and credit. If they see that the difference is $1 as you say, they might agree to do that and save some time. But if they come back and say "please amend your return", then you'll have to do that - but give them the chance to do the correction, since they have the power to do so.

Again, I can't see the letter you have received, but from the description, your tax return processing and your refund is being held up until this matter is cleared up - another reason to give them the option of just correcting your return for you.