We do not pay FICA for our employees. Those who are required to pay FICA must pay "both halves" of the 15%. Our pastors have all chosen to be exempt. We had to file form 8274 to do this, which we have done.
In 2010, on our W-2 forms, Box 3, Social Security Wages, we put the total wages for our employees, and in Box 4, we entered 0.00 because we withheld $0.00 from our employees.
It turns out, we should have left box empty and box 4 empty.
The IRS compared our W-2s to our 941 quarterly reports and found the discrepancy between the Social Security Wages reported on the W-2s and the 941s.
The letter from the IRS (which came in April 2012 for the fiscal year 2010), said we owed $29,000 for Social Security withholding. (it could have just as easily said we should have left box 3 empty, but it did not).
I have learned not to panic over such letters. We called and got a hold on the penalty and filed amended W2s and W3s. It took about 1 year for the IRS to receive and process them.
Since we made the same mistake in 2011 and 2012, we filed our amended W2s and W3s in anticipation of them finding out. That didn't stop the nasty-grams from coming.
We received another letter in May 2013 about fiscal 2011 being incorrect, a threat to place a lien on our bank accounts and an amount due of $22,000.
I called, got the hold placed on the penalties, and told them about that we already filed the amended forms. It is now 2/19/14 and they won't have the 2011 amended forms processed for 7-9 months from now. Each hold is only 9 weeks, so I need to place a reminder to myself to call and have the hold reapplied every 9 weeks.
Then, about a year from now, they will get around to the 2012 returns and amended forms, and the process will begin for that year and probably get resolved in 2015 or 2016.
If you have a letter from the IRS, please don't panic. Call them, take good notes (get the name and ID number of the representative). They have always been friendly and helpful. I don't know who sends out the letters, but it's not the same group of people that you get when you are on the phone with them.

That's my story. Hope it helps.