Moving to InDesign EPUB forum
What version of InDesign? Reflowable or fixed layout EPUB? What functionality are you looking for in those footnotes?
reflowable text layout and something simple for the foot note. Not sure what the options are. I'm working with the latest version of InDesign
What exactly do you want?
InDesign is certainly capable of foootnotes but they get converted to end notes or placed at the end of the paragraph in relfowable EPUB. You can also choose to make them pop ups though that feature has limited reader support.
These choices are made in the EPUB export dialog.