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That cite is a good reference. Importantly, you need to confirm whether Form 4361 was filed by the priest. My guess is that is was long ago. So the OASDI and MC withholdings were wrong. I'm not sure whether the priest wanted state withheld, too. As a church treasurer for 7 + years and still involved, every minister here has wanted federal and state tax withheld and the local tax was required. What to do now? I seriously doubt that you can get it refunded but suggest that your church try to make the priest whole and, of course, check to see what has happened the rest of the year. Check the Paychex to see if they have any solutions. Is it possible to 'reassign' these erroneous withholdings to a lay employee before W-2's are prepared and the last pays are made? It's hard to imagine that Paychex was not apprised of the clergy status here. A few years ago we began using Paycor and they have been great with all the quirks involved.

I am not an expert in clergy, having only 2 clergy as clients. See if this IRS topic is helpful. https://www.irs.gov/taxtopics/tc417

And we get an extra 9% from state for a big night out on the town.