OK ... did the payment with the extension NOT show up on line 10 of Sch 3 ? If it did then you got the credit correctly on the tax return.
If it did not show on Sch 3 line 10 did it show up on line 8 ? If so you did get the credit but on the wrong line ... If that is what happened then review that notice again carefully ... are they telling you the amount was on the wrong line ? The IRS usually figures out these kinds of mixups eventually.
Give the number on the notice a call and let them explain what happened ... ask them about the extension payment if needed.
