Footnotes in EPUB export can be fragile. There are three things to try:
Close InDesign, then open in, immediately open the book file, and then try the export without doing any other operation (edit, reviewing, changing settings, etc.) I've had this workaround be effective too many times to count, especially with large or complex files.
Then try the general InDesign 'purge': export the document to IDML, then open that file and save it as a new INDD file under a new name. Re-try the export (again, as soon as you open the new file). That purges ID files of corruption, bloated content from undo, etc. and rewrites the structure, and often fixes prolblems with long-edited files that can have all kinds of small corruption faults.
Then try Rishabh's suggestion: export subsets of the book. Create a copy, delete the second half, try the export. No problem? Repeat and delete the first half. If one half or the other exhibits the fault, repeat the "by halves" process — ON FILE COPIES! — until you isolate a few footnotes that are apparently causing the issue. Then check all of those carefully.
If none of that works, report back, and be sure to specify your platform, OS, ID version and what EPUB export format and settings you're using.