It's a mistake, you need to fix it. Fill out and give them a new W-4.
You are not eligible to be treated as a "religious worker" unless you perform sacraments and other religious duties similar to a minister or pastor. But, if they withheld tax in box 4 and 6, then they didn't treat you as a religious worker anyway. It just sounds like they entered the wrong code for your federal withholding when they put you in the system.
Alternately, your withholding is correct for what you told them. If you told them you were single with kids, or married with kids and your spouse had no job, then zero withholding would probably be correct. A single parent with 2 kids filing head of household would owe no federal income tax on the first $50,000 or so of income. So it sounds like you had more than one job, or you claimed too many exemptions on the W-4, or you have a spouse who works and you didn't take that into account.
Or possibly, you made a typo with your income when entering your W-2 in Turbotax. Or possibly the W-2 is wrong, did you in fact have federal tax withheld from your pay checks that is not showing up in the W-2?
When you prepare a new W-4, and you are married with a working spouse or you have more than one job, you have to complete the form and calculations one time taking all factors into consideration, then file new forms at all the jobs. For example, the instructions might say to claim married with 1 exception at one job, and single with no exemptions at the other job. Form W-4 has 4 pages of instructions and worksheets, not just the front page you turn in.
