Do the numbers reset to 1 at every chapter? Not asking because that'd have caused the problem, but because the solution might be more complicated if they don't.
What's supposed to have happened is: the number should have appeared in that <a> at the front for the backlink, but it's empty. You can wrangle a fix by shoving that <a> to the end via regex and filling it with e.g. an arrow or something. That way, people have something to click on to get back, since the numbers are missing. Then you can do something semi-similar to transform the notes section into an <ol> to get the numbers regenerated. Those new numbers won't be linkable though, which is why you need that arrow at the end too.
But that won't work well if the numbers don't reset at every chapter, because e.g. <ol start="11"> doesn't work reliably for ebook. I can probably whip up an example for what I'm describing above, or maybe others will have better ideas.
In InDesign, you might doublecheck that Numbers: Map to Ordered Lists is set under the Text section of the epub export options. Or if it is, see what happens if it's not. It's worth a check since it's relatively quick and I guess it could cause something like this.