Did he only receive one W-2 Form?
If so, the issue is that he was technically treated as an employee until he was ordained. He probably had social security and medicare tax withheld on his earnings while he was an employee.
When you report any housing allowance within TurboTax, you report self-employment income for the housing allowance and the portion of the time you are treated as being a member of the clergy. However, the Social Security and Medicare taxes being filled out makes it seem like he is an employee and not a clergy member entitled to the housing allowance. Hence your error message.
There are 2 ways to go about this.
1) Contact his employer and ask them to issue corrected W-2 forms, one form which shows only the W-2 income when he was treated as an employee and had Social Security and Medicare taxes withheld; and the other W-2 showing his income once he became an ordained minister and had the housing allowance.
2) If you cannot get corrected W-2s, and you know how much income is from his time as an employee versus the amount of income he was an ordained minister, you can separate your input into two different W-2 Forms and reflect each scenario. Be sure to make a note that you had to separate the W-2 forms to reflect the different types of income.
Also, if he has filed Form 4361, Application for Exemption from Self-Employment Tax and received approval from the IRS, he may not be subject to Self Employment tax on his earnings as an ordained minister.
Form 4361 exemption application
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