Okay, many things to consider.
First, it looks as if you are exporting to Fixed Layout EPUB (FXL). Fixed layout is... more or less an obsolete format, best used for image-based books like children's books, graphic novels and "art" books where the composition of the page is critical. If you can, you want to take advantage of e-book/EPUB's features by exporting to reflowable ('liquid') format.
EPUB is also highly dependent on the reader, to the point where it borders on anarchy. There is no standard EPUB reader; there are those that hew closely to the actual standard and then the many that loosely interpret the standard and 'fix up' a lot of features to suit their user base and idea of how e-books should work.
Apple's reader, unfortunately, is quite an outlier on this spectrum; like most of what Apple does, it's very much to their ideas and notions for the closed universe of iBooks, and not reliable with the general run of EPUB books.
The short version is that you either need to choose one 'proprietary' platform (usually iBooks or Kindle) and optimize the EPUB for it, and let everyone else just cope, or optimize your EPUB for one of the standard readers (Thorium or Calibre), then try to tweak it for parallel compatibility on iBooks but otherwise let users the proprietary/outlying readers deal with any book or display anomalies.
Put really short, export to EPUB is nowhere near as bulletproof and reliable as export to PDF. It takes work on the document and on the export process to get an acceptable result for some subset of apps and users. And no, it's not much to do with InDesign or its export process; the plethora of freeware tools have much the same issues overall.
I'd start by trying to get a good reflowable export that displays in Calibre well.
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