Several thoughts:
1. The $1,000 add-on for being 55+ is prorated for the first year you turn 55. Think of it as $83.3 a month for each month you are 55. So if your wife turned 5 in 2023, your limit is not quite $8750.
2. It is OK that her contributions are payroll deductions - in fact is more common than direct contributions.
3. Please tell me what month your spouse turned 55 in, and also her code W value on her W-2 in box 12, and also any contributions you made (direct or payroll) to your HSA.
4. With the numbers you have given us, I can't quite figure out what TurboTax is thinking, but I have done HSA answers for 8 years, so we will be able to figure it out, with enough input.
5. It looks like you already realize that your Self-only HSA doesn't really count for the limit - good for you.
I look forward to hearing from you.
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