What made you think this is an InDesign problem? Seems to me it's a fault in your ePub viewer. Just try another one.
This is the ebook reader (epub) default apple, my ebooks will be sold on the apple store so I can not change the reader.
Highly technical EPUB questions like this are probably best posted on the MobileRead Forum where a lot of EPUB developers hang out. While there are some beginner to intermediate EPUB users here, you'll probably have better luck there.