Here is the statute for calculating the earnings on the excess contributions - here. Yes, it says for IRA, but the calculations are the same as for HSA.
You are correct that when you make excess contributions, when you request the "withdrawal of excess contributions" from the HSA custodian, that the custodian should also calculate what the excess earned while it was in the HSA and add that to the 1099-SA to be sent to you.
Ask for a supervisor at your HSA custodian, because there is no reason you should have to do this calculation.
If they refuse to make the calculation, use the link at the top to do it yourself, and document this situation so you can tell the auditor how your HSA custodian fell short on the job if you are ever audited.
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