Retirement tax questions

Hello, my husband is a pastor and we have been struggling doing out taxes for 2018. We filed for an extension because we just couldnt figure it out and we dont have the money to pay for someone to help us. Here is the situation: we were told we HAVE to pay self employment tax on both HOUSING and INCOME. So I selected that on my Turbo Tax, however, at the very end it always wants me to review that section and it tells me I shouldn't have the housing selected if I have had either social security tax withheld OR medicare tax withheld. 

 

Our tax person made an error, and we had Medicare taxes withheld, but because there is an amount in that box, turbo tax is acting like we shouldnt have the housing selected, so when i uncheck that box, we literally go from owing like $300 to getting an $8000 refund. We were told to just pretend and ignore the fact that we had Medicare withheld, but that makes me confused, because it was withheld.