You have one overall HSA limit for the entire year, no matter how many accounts it might be divided between. If you made excess contributions, you need to remove them by April 15. You must also remove any earnings that are attributable to the excess contributions (interest, investment gains). The HSA bank will know to do this, but you must ask for a removal of excess, not a regular withdrawal. It does not matter which account you remove the excess from. It can be your money or the employer money that you remove, you do not have to pay it back to the employer.
When Turbotax calculates you have an excess, the excess contributions will be automatically added back to your taxable income. If you indicate you removed the excess, you will not be assessed an additional penalty (if you do not remove the excess, it is subject to a 6% penalty that recurs every year the excess is in the account). The attributed earnings are reported as miscellaneous other income on your 2024 return, even if the earnings are paid in 2025 when you make the withdrawal.
