What InDesign version? What operating system?
if you have the latest version of cc2017 you can span footnotes across two or more columns in a multi column text frame (one text frame with two or more columns)
(if you have two or more single column text frames in this case you can't span footnotes)
I suspect that’s what’s happening here. Thanks.
James F. Smith
[Removed by moderator]
Best not to post personal data on these public forums.