We have figured out how this is most likely happening: when creating a copy of a document, the sidebar is unable to detect duplicates until the document has been formatted at least once. The current best workaround is to always run “Update Citations and Bibliography” after making a copy of a Google Doc.
For existing errors, please remove all in-text citations, go to the gear in the sidebar --> Manage references. Then remove one of the duplicates and re-insert the citations.