TurboTax is reporting this correctly based on what is on your W-2. The reason you do not see a reduction in your Box 1 wages for your HSA contributions like you do for your 401(k) contributions is because, unlike your 401(k) contributions, HSA contributions also reduce your taxable wages for Social Security and Medicare taxes. That means the Box 1, 3, and 5 amount have been reduced by your HSA contributions.
Since you have already received the benefit of having your wages reduced by the contribution for these paycheck deferrals, they are reported on Form 8889 as employer contributions, even if they were something you elected to do. You only enter contributions you personally made out-of-pocket with post-tax dollars on Line 2.
I suspect if your 2020 Line 9 was $1,000 and Line 2 was $7,000 then you may have had an over-contribution in 2020. Also, either your W-2 for 2020 had $1,000 in Box 12 Code W or it was reported incorrectly on your taxes.
