The direction of each subpath—the order in which its points were created—determines whether the area it defines is inside (filled areas) or outside (empty). If, in your compound path, holes sometimes don’t appear where you expect them to, you can reverse the direction of that subpath.
In Illustrator, in the Attributes panel, click the Reverse Path Direction Off button or the Reverse Path Direction On button.
In InDesign, choose Object > Paths > Reverse Path.