This is a common error amongst churches, parachurch organizations and seminaries. First, I would inform your client of the error since ultimately they are responsible for following the IRS laws. Some churches, etc. simply refuse to follow the law, sadly. The client can then approach their employer and advise them of the error. Sometimes it is simply because they are unaware. IF the employer refuses to correct their handling of the social security tax, I document such in my file to protect myself. Then in order to get the software to handle the numbers correctly you have to NOT enter the housing in as a housing allowance. You have to enter it in as untaxable income. The software will not allow a housing allowance AND FICA for the same person because it recognizes that it is incorrect.