What were they doing incorrectly? It is hard to imagine a church not understanding clergy taxes (yuk, yuk), or a clergy member not being satisfied with the tax laws in place (totally serious on that one). I guess the problem is the senior pastor, and not your client in your case, though.
I had a pastor come in yesterday with info to complete 2009 - 2012 returns and a note to call the church treasurer so he could explain housing allowance rules to me. Yeah, I'll get right on that.
She also had an unopened, returned 2007 return, apparently the IRS PO Box was closed by the time she got around to mailing her return. It was returned in 2009, and she hadn't bothered to call or anything. I opened it, noted no check to IRS, gave her a new envelope, said, "Hey, you really ought to put a check in there for Caesar, Jesus said to do that, right?"
She laughed, "Shut up, I know."
I thought, "Oh, so you knoweth to doeth good, and doeth it not." But, I just let it go... I keep chanting that these days. Let it go. Let. It. Go.