It may be a typo or something might be doubling up. Take a look at the SE Adj Wks to see a breakdown of the amount on line 2 of Schedule SE. Did you check the religious employment box in the uncommon situations screen after you entered your W-2?
You may need to make an adjustment if your housing allowance was included in Box 1. See the 2nd help article below for instructions on making the adjusting entry.
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