The first question is what is your Medicare start date? If it was June 1, 2025, then you were eligible for 5 months, and your contribution limit for 2025 would have been $2208 if you were covered by single insurance or $3979 if you were covered by family insurance. It is the amount that counts, not when in the year the contributions were made. For example, if you and your employer contributed $200/month for the whole year, you would be under both limits, and not be required to remove anything.
In the HSA interview, make sure you answer that you did not have qualifying insurance all year, and then click the boxes next to the correct answer for each month (single, family, or none). Turbotax will calculate your limit.
You must report all contributions made in 2025 on your tax return. Contributions made by payroll are captured from your W-2, this includes both employer and employee funds (all payroll funds are technically employer funds and are on the W-2). If you also made separate contributions you list them in the HSA interview. Turbotax will tell you "you have excess contributions, will you remove them before the deadline??" Answer yes.
If the return of excess was made in 2026, you will not get an adjusted 1099 for 2025. Just answer "yes" and turbotax will remove the excess it calculated from the form. Then, you need to report any interest that was returned to you as income -- it is 2025 income even though it was paid in 2026. You can enter it in the Interest Income section and check the box for "this interest is not on a 1099-INT".
If you removed more than the calculated excess, post back here for a followup. That is a trickier situation because Turbotax calculates the excess based on the rules and if you withdrew more than you should have, that is not automatically handled by the program.
