When it’s clear someone has a concern, the longer it takes to get the concern out of them, the more likely there is that there’s other concerns still sitting behind that one.
Once you’ve started digging, and they’re opening up about the issue they have with you, or church, or whatever… squeeze the pus. Keep creating space to let them get it all out. Keep thanking them for their opinion, thanking them for having the guts to come and talk to you, keep asking if there’s anything else.
It might even be worth getting to a certain point and writing it down; “So you’ve raised a few issues… first it was X, then you raised A, B and C. I’m really glad I got to hear those. Is there anything else?”