It's hard to say exactly whats going on without seeing the part, but this is my best guess.
You have part A, with the original hole. Some surface (either the cylindrical surface of the hole or the planer surface with the hole in it) is waved into part B. Since their is a wave relationship between the two parts, the location of the hole in part B, is controlled by the hole in part A, essentially locating it. Now, you are attempting to mate part A to part B (or part B to part A), which will again try to locate the hole, thus creating a conflict, ie you can't locate the hole twice.
As an experiment, try this. Break the wave link(s), and then try to mate the components. This should determine if the wave link is causing the conflict. And/or mate the surfaces of the components BEFORE creating the wave link.
-Dave
Everything should be designed as simple as possible, but not simpler.