I've never had any sync issue using nextcloud myself.

The multiple files are because Joplin doesn't just sync your plain notes, it syncs note revisions and changes to notes. So I suspect you are syncing revisions as those extra .md files. This also includes deleted files which only get removed once your note revision period has run out.

Is the attachment definitely in Joplin and not just a local reference? i.e. it got a Joplin generated id as the filename?

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