Dear respected,
Welcome to the Microsoft Community.
Based on the description, we tried to deploy the same environment and we found out that we can reproduce a similar behaviour that adding a footnote will be shown in bottom right which is on the left column but not right column. And also, when you add a second one, it will show bottom in right column, but the footnote line only shows in right side.

In this situation, we may be sorry to convey that this is by designed and kindly share your valuable idea to the product development team so they can hear your voice and improve for a better user experience. How do I give feedback on Microsoft 365? - Microsoft Support
Appreciate your patience and understanding and thank for your time and cooperation.
Sincerely,
Mia