Yes, you are correct. Even if your income was above $400,000, that line would still be $2,000 for you. The reduction for incomes above $400k doesn't come until lines 11 and 12. If your child qualifies for the child tax credit, your line 5 amount should be at least 2,000. If they don't, it should be 0. I'm not sure how they could come up with 1,000. Take a look at the Line 5 worksheet.
Could they be challenging a different number on Form 8812 or saying that your child does not qualify? The only thing that comes immediately to mind is if you received advanced child tax credit payments and did not report them on Line 14f.
