Try trashing your InDesign preferences.
Please re-try after trashing your preferences as mentioned by Derek.
If issue still persist, I would recommend you to package your document and share it with me for investigation purpose.
Share with firstname.lastname@example.org
To reset your InDesign preferences:
Close InDesign and relaunch it, and IMMEDIATELY hold down Ctrl + Alt +Shift (Windows) or Cmd + Ctrl + Opt + Shift (Mac), and respond with Yes to the dialog asking if you really want to replace the preferences.
If you aren't asked the question, you didn't hold down the keys quickly enough!
Is your ePub a reflowable text ePub or a Fixed Layout ePub?