"Then after adding my wife's HSA/HDHP details, it switched me to Family on line 1 of my 8889. "
Are you sure that neither one of you indicated Family as your HDHP coverage? TurboTax can handle the situation where two spouses each have separate Self-only HDHP plans, so TurboTax did not "switch" you to Family. Please review your entries.
As an aside, when one of you have Family HDHP coverage, then both of you have Family HDHP coverage for purposes of the 8889, no matter what coverage the other spouse had. TurboTax will allocate the Family HSA contribution limit as needed (you can see this on the 8889-T and 8889-S).
"How do I account for withdrawing too much in TurboTax since its probably too late to put it back?"
You can contribute to your HSA under the 2024 limit until April 15, 2025. NOTE: when you make this contribution you MUST tell the HSA custodian that the contribution is for 2024, or the HSA custodian will assume that it is for 2025. You would be wise to check this after the contribution has been made.
However, when all is said and done, you would be better off letting TurboTax tell you what your excess contributions are, and letting the HSA custodian calculate the amount of earnings on the excess. That is, when you are doing your tax return in TurboTax in the following year, TurboTax will advise you of any excess contributions. Then you are to contact the HSA custodian and ask to withdraw an excess contribution of X amount. The HSA custodian will calculate the earnings, and send you a check for both the excess and the earnings. The custodian will also send you - sooner or later - a 1099-SA with the total amount on it in box 1 and the earnings (included in box 1) in box 2. Box 3 will show a code of 2.
So tell us what you actually entered.
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