PDF fluke where the <Reference> and <Note> tags appear out of order for no reason

Hi all,

This one is driving me crazy and I can't find any help online. I'm remediating another designer's document. I have the source InDesign file and it looks like it was created properly. However, in the exported PDF none of the <Note> tags are linked to their correct <Reference> tags. See the screenshots below: Footnote 11 on page 28 has the correct <Reference> but its companion <Note> tag links to footnote 16 on page 60! Every single one of these is totally jumbled. I'm not about to manually move tags in this 100+ page document. Someone at Adobe please comment. Thank you.