A designated housing allowance is exempt from income tax. The rest of the retirement income is always subject to income tax. During the pastor's working life, both the housing allowance and salary are subject to SECA (even though the housing allowance is excluded from income tax), but in retirement, neither is subject to SECA. You appear to be entering the retirement income as if it was compensation earned from working, and getting charged SECA when you should not be.
The retirement should be reported on a 1099-R, did you get any tax forms from the plan that is paying the pension? How is the retirement income being paid and do you get any tax paperwork from the denomination? If the denomination is issuing a W-2 or 1099-NEC, the denomination is indicating that the payment is compensation that is subject to SECA, and you need to contact the denomination to straighten it out.
Here is how to report the retirement income if you are receiving a 1099-R.
https://ttlc.intuit.com/turbotax-support/en-us/help-article/retirement-benefits/enter-parsonage-hous...
The Pastor is not permitted to deduct clergy-related incidental expenses because the pastor is not reporting compensation (wages) for services performed. If the pastor reports compensation, they can deduct expenses related to the work they were compensated for, but must follow the Deason rule. (They can also only deduct expenses directly related to the work they were compensated for, they can't deduct general incidental expenses of being a clergy member that are not connected to particular paid duties.)
