To answer your last question, in TurboTax, in the HSA interview (go to it manually if TurboTax doesn't take you there), you will start the HSA interview for yourself and when you are asked "Did [name] have covered by a High Deductible Health Plan in 2023?", answer "Yes, I was covered by an HDHP at least one month a year".
An additional question will appear, "What type of HDHP covered did [name] have during 2023?" Click on "I had different plan types at different times of the year".
This will open a new screen, in which you can check "None" for HDHP coverage for each month of the year (remember that Opus pointed out that you cannot have HDHP coverage when covered by an FSA). Yes, you had HDHP coverage, but this is how you disqualify it in TurboTax.
Then click on Calculate Max Contribution limit at the bottom. The next screen - looking very similar - will appear, with "Your maximum contribution limit is $0".
Now continue with the interview. Any HSA contributions by you in 2023 will be declared to be "in excess", and you should agree.
NOTE: if your HSA contributions were made through payroll deductions, then the excess will be added back to your income. However, if your excess contributions were made by direct contribution to your HSA (not through your employer), the excess amount will simply not be added to Schedule 1 (1040) so it's not deducted from your income.
TurboTax automatically handles this situation; please do NOT try to fix this yourself.
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