Amazon's Kindle Previewer assumes that content which is organized using pairs of matching forward and back links is a footnote and should presented as a popup when the forward link is clicked. This works correctly in most cases but as your EPUB demonstrates it can cause problems if forward/back link pairs are used for navigation within a book's content.
You can fix this by changing the page layout so that forward links do not link directly to back links. For example by changing :
| PreviousSect | HomeIdx | NextSect |
to instead be:
| HomeIdx | PreviousSect | NextSect |
|