If I'm understanding correctly, the $1,000 reported on your W-2 includes both employer contributions and contributions you made, I assume through diverting money from each paycheck into your HSA. Regardless of whether it was funded by your employer as some kind of match or benefit or by you as a voluntary contribution to your HSA, it is reported the same way on your taxes, on your W-2 as Code W.
Either way, it got there before the contribution was taxed. TurboTax is trying to differentiate between a contribution was with pre-tax dollars or a contribution paid out of pocket with money that has already been taxed. If it is the latter, then you would receive a deduction for the contribution. If the contribution was pre-tax, then you already got the deduction because you are not being taxed on that income.
If the Code W on your W-2 is not correct, then you would need a corrected W-2 from your employer that only has their contributions. This would be the case if you received your paycheck, then deposited a portion of it into your HSA.
If your employer handled your personal contribution by sending a portion of your pre-tax income to the HSA, then the W-2 is correct and should not need to be overridden in TurboTax.
