Also: Was the file attached or entered into some kind of database?
One alternative plausible explanation apart from Syncthing having a bug could be: you having missed to ignore some files/folders (e.g. Zotero) that should have been ignored, which then led the database to create dublicate files during or after the sync.
e.g.: “Storing the Zotero data directory directly in a cloud storage folder is extremely likely to corrupt your Zotero database and should not be done.”
(because i saw Zotero in your ignore folders…Syncing Zotero files is a big hit on my wishlist as well. Maybe one day i will try a setup, but for the time being, since it seems so complicated to implement, is not supported well by the developers and i don’t derive enough income with that work to opt into the paid version, i am using Jabref as a workaround.)