I'm not certain that you should have received a 1099-MISC for contributions to an HSA. You should contact the church to correct the Form W-2. HSA contributions are reported in Box 12 with a code W on the W-2 form.
If you cannot get the church to correct the W-2, then you can enter the contribution in the HSA section page, Did your employer tell you about any other contributions?
See attachment.
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