We're using Turbo Tax Deluxe desktop. MFJ Ages 64 and 62. Turbo Tax only asks if we had a HDHP for all the months of 2024 (and I filled in Self Plan for each month) not 2025. Then the $5299 and $5296 contributions do not show up as deductions for 2025 in the summary. The comparison with 2024 shows those as deductions but for 2025 it says "0". In the Federal Review it has approximately $10,000 less deductions for 2025 as opposed to 2024, so it seems like that is the problem, when everything is about the same as last year.
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Please clarify whether your contributions to the HSA were reported on your W-2 or if they were entered separately.
Also, if you would be willing to share a diagnostic copy of your tax data file it could be helpful to take a closer look and see what might be happening with your return. The diagnostic file will not contain personally identifiable information, only numbers related to your tax forms.
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HSA contributions were reported on the W-2
If the HSA contributions were reported on your W-2 in box 12 with code W, then they will not show up on Form 1040 Schedule 1 line 13. The contributions reported through your payroll are already funded with pre-tax money and cannot also be deducted on your return. If you made the HSA contributions yourself, outside of your payroll at work, then the contribution can be deducted because it was made with after-tax money.
Be sure that when you go through the HSA section of your return that you see onscreen the amount that was reported on the W-2 in box 12. The HSA contributions will be reported on Form 8889, which also confirms that you were eligible to make the contribution based on your High Deductible Health Plan (HDHP) coverage for the year.
As for the difference between last year's return and this year's, take a look at the 2024 Form 1040 Schedule 1 line 13 to be sure whether the HSA contribution was actually deducted in 2024. If it was and it was also reported on your 2024 W-2, then you should amend the 2024 return to remove that deducted contribution.
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