In case anyone else has been baffled by skipped figure numbers, I may have the answer. In a book manuscript I’m working on one chapter at a time. I keep finding skipped figure numbers, and tracked it down to having a cross-reference to a figure in an earlier chapter in there. I fixed the problem by unchecking “Treat compile group as complete manuscript” in the first compile panel; then it goes back and catches the cross-references.
Now I know what that checkbox means!