Sometimes scripts that automatically generate .epub files end up creating files that make ebook readers cranky.

Are you comfortable using Calibre? Sometimes converting the ePub file to another format, deleting the original ePub and converting back to ePub will fix the problem.

I haven't had this issue with AO3 files but have had it with files that were initially converted to ePub from DAISY. Darn things kept crashing my Sony until I tried running them through Calibre.