Hey, welcome to MobileRead!
You're probably going to have to give more info though. Can you:
1. Attach a sample EPUB with the problem?
2. Give the footnote code + HTML.
It could be something with the way you coded it, or it could be a bug with Apple Books.
But if give that info, it'll help others test + mess around and see if we could figure it out or explain a better way.