Answered on https://www.reddit.com/r/elementaryos/comments/7jmf2n/duplicate_songs_in_noise_and_lollypop/dskadbd/
I noticed this happening when I import music with the "Import to Library…" menu item in settings. I figure it could be a matter of the "Copy imported folders to Library" preference where the program could be importing a folder and adding it, then see the files copied in the library and show those too.
In fact browsing the sqlite database shows the double entries one with a path in ~/Music and the other at the original path where they were imported from.
I haven't delved much into trying to debug this since I have to rebuild the library every time and it's time-consuming, but since Noise seems to have added the copied files on its own I just disabled "Copy imported folders to Library" and started manually moving files into ~/Music, the changes will be reflected automatically in my Library.
disable copying to library and move files by hand to ~/Music
(or wherever your music library is)