The software is incorrectly capturing my HSA contribution as non-deductible. How do I make it deductible?

The HSA contributions reported in box 12 of your Form W-2 is not deductible on your tax return.  That is because the funds that were contributed to your HSA are pre-tax.  The amount is not included in your W-2 wages.  Since it hasn't been taxed, you cannot deduct it.  

As explained by The HSA Store The Deductibility of HSA Contributions:

Employer contributions to an HSA are not considered income, so they're not subject to income tax or payroll tax. If the employee makes contributions via a Section 125 salary reduction arrangement, those contributions are also considered employer contributions, meaning they're not subject to income tax or payroll tax; these contributions show up in Box 12, with Code W). 

[Edited to add citation 02/16/25|11:15 pm PST]