Hi,
I you are using quicksubmit, it could be this: [OJS] QuickSubmit in OJS3 breaks custom_section_orders · Issue #2376 · pkp/pkp-lib · GitHub
See also OJS 3 Articles appearing in the wrong section in the Table of Contents
I have fixed this by removing all entries from custom_section_order that have the issue_id which has problems. After applying the fix in Github, I have not heard of our journals the similar issue.