Comment by starkparker

Reflowable epubs in InDesign require discipline that a lot of print designers (and even some full-time typesetters) lack. You have to use a single content flow (all text must be linked between text frames in one unbroken flow), any images and sidebars must be anchored in that flow (you can't just freely place them on the page), and you have to consistently use paragraph and character stylesheets (i.e. you can't just ctrl-B embolden text, etc., you have to create/use a "Bold" character sheet).

It's hard to call that "difficult" because those are already best practices for print, but they aren't intuitive to most people and InDesign doesn't make it easy to track how much of this you're doing correctly or flag which parts you've done wrong.