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No direct experience with HSA over contributing, but have done this with Roth IRA.
The act of spending some of the HSA Money during the year does not fix the over contribution, if that is what you are asking. Also small is a relative term. You have to contact the HSA provider and ask if they can remove the over-contribution along with it’s gains. You may be subject to a 6% excise tax every year until this is fixed. So depending on the amount you should take action.

If your employer did this through payroll deductions causing the overage , they may have already fixed this and you would see this on your W2. If you made contributions on your own then you need to fix it.

In the case of the Roth, the options were to remove the overage and earnings, or have them recharterised as a Non-Deductible-IRA contribution. I do not know if the HSA has this option or not.

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