Duplication can occur in the event of a sync conflict, where you try to modify an item which already has pending modifications that haven't been applied yet. Sync conflicts are rare, but can occur when using Standard Notes on multiples devices with differing network connectivity levels.
Typically, with normal non-encrypted applications, the server handles sync conflicts automatically, so users don't always notice it. However, due to the encrypted nature of Standard Notes, our server cannot read your note contents, so cannot automatically resolve conflicts. Instead, conflicts are handled on the app-level, usually by duplicating your note if there are any differences between the two copies.
You can avoid duplication by ensuring a healthy network connection when using Standard Notes, or by making sure to pull in the latest changes before modifying an existing note.