The issuer of the 1099-R is only concerned with reporting money Out. Not with what happened afterwards or if your taxpayer didn't take all necessary actions.

Since the taxpayer removed only $6,000 of the $7,000 and assuming there is growth or earnings in the account attributable to the excess contribution, you have two conditions. And over two years.

There still is an ineligible contribution of $1,000. Plus any earnings attributable, which get reported as taxable income. That contribution and the earnings are subject to a 6% penalty for tax year 2024. And if they don't correct it for 2025 tax year, it's penalized again for 2025 and new earnings are taxable.

Here's some guidance:

https://www.fidelity.com/learning-center/smart-money/overcontribute-to-an-ira