If you want to leave the funds in the account and pay the penalty, it sounds like there is an error on the HSA worksheet. Try going back to the HSA interview in the Deductions page, and change your answer to "No" when it asks if you had qualifying coverage, or check "none" for all 12 months of the year. (Even though you did have coverage, you were ineligible for other reasons, and you need to answer "none" on that worksheet for the program logic to make sense.)
You will have to do that even if you do remove the excess, I think, because that cross-check between insurance coverage months and dependent status will still occur.
But as noted, you have until October 15 to remove the excess, as long as you properly filed for an extension before April 15. (If you did not file for an extension and are just late, then you are too late to remove the excess and you must pay the penalty.)
Then we also have to talk about 2025 because you may be assessed another penalty unless you take corrective action before December 31, 2025. But you have several options depending on your situation.
