I withdrew my 2024 excess HSA contribution in early 2025, so my W2 does not reflect this withdrawal.

Was this an excess reported by TurboTax while doing your 2024 return (or was it from 2023?).

When TurboTax told you that you had excess contributions, it gave you the option of withdrawing all, some, or none. Which did you choose?

The penalty is applied only to excess contributions that you did not withdraw. These will be carried over to line 2, form 8889 on your 2025 return, and you will be charged a 6% penalty on the carryover. In this case, be sure to reduce your HSA contributions in 2025 to allow for this carryover.

So please confirm that these were excess contributions from tax year 2024, and tell me what you told TurboTax about the excess:  withdrawing all, some, or none.