1) Missing the book cover inside them, it should be on the first "page" of the book. If missing, your title page will become the cover when viewed in the reader's library shelf.
2) Using embedded non-standard fonts.
3) Fixed layout pages, including 2-page layouts. You can't read these on a cell phone screen because your fixed layout gets shrunk to fit.
4) Though your self-created epub may pass EpubCheck, you should test it in Adobe Digital Editions and on your smartphone and tablet Epub-reading apps.
5) Not critical, but doesn't look as professional, missing or inaccurate metadata in your Epub such as Book Title, Author Name (shows as "Unknown author") and short book descriptions. This is all data used by ereaders for sorting and search results.
Distribution to dozens of retail outlets requires compatibility on many devices and ereader apps. Text should "flow" and be re-sizable by your customer as well as able to conform to the "Night Reading" setting (white text on a black page). Also test if you can search for a word in your epub and highlight and add notes to the text on an ereader app.