PDF has absolutely nothing to do with ePub. You can have a PDF which looks fine where as the ePub isn't.
Unfortunately creating ePubs is not intuitive and has a steep learning curve.
You might be interested in watching some training-videos from video2brain.com or lynda.com first. Further more to help you we might be interested in your InDesign-Version and the kind of ePub you like to create (ref. or fxl or ...).
Thank you for answering. I did the trainings on lynda.com but the videos do not cover my problem. I work on Indesign CC 2014 for Mac and want to export in a refloating EPUB.
What I did find out so far is that the problem must have to do with the definition with the paragraph style. When I re-fine the title from title style back to normal paragraph style - or also if I change it to a higher level title style (level 1 instead of level 2), the order of the exported EPUB is again ok.
Can you provide an example (InDesign Document) with the wrong order on export?
Do you export ePub 2 or ePub 3?
Real lists or converted to text?
Did you structure your text flow using the article panel, xml-structure or text threads only?
I use ePub 3 to export, lists are real lists and I tried both, article panel and text threads, both deliver the same result.
The link leads to my dropbox with three files: the Indesign document, the pdf with how it should be and the EPUB with the disorder.