One thing to check in the software is whether the type of coverage is coded correctly as "Individual" or "Family" because the limit on contributions is higher for family coverage. That's something the client needs to tell you - if the HSA contributions were made via an employer, they would not allow a mismatch between the type of coverage and the contributions, but if the HSA contributions are being made personally, then you need the client to verify the type of insurance coverage. The HSA custodian wouldn't know the type of coverage.
If there really was an overcontribution, you should discuss the options with your client - to remove the excess contribution tax from the return, the client will need to withdraw the excess contribution from the account by 4/15/2025. It's really the client who needs to make the choice as to how to proceed.
When this happens to a client of mine, I wait to finalize the return until they provide a copy of the withdrawal paperwork from the HSA custodian, to be sure it gets done before the return is filed.