No idea how else to explain than to show this:
It should be mirroring it, but for some reason the other side comes out really weird. And not just this part. There are other parts, too.
Out of interest in rearranging modifiers, moving the shrinkwrap modifier before the mirror and hiding the mesh makes the holes disappear that would otherwise be there, but the mirroring is messed up if mesh is enabled in that the "keep above surface" on the mirrored side doesn't work:
Again, it should not happen, but it is. Any help would be greatly appreciated.