There are a couple of options for addressing duplicates on your iPhone.
You can delete the duplicate songs directly from your iPhone:
Remove a song that’s been downloaded. Swipe left, then tap Delete.
The alternative option is to enable manual syncing when your iPhone is connected to iTunes and search for and delete the duplicates.
You can follow the steps in this article to enable manual syncing:
Once you have that enabled and your iPhone selected in iTunes, you can use iTunes' feature of showing duplicate items so that you can see them all at once and delete the duplicates that you want to remove:
Choose View > Show Duplicate Items to show duplicate items (matches are based on the song name and artist). If you have multiple versions of the same song (for example, live and studio versions, or versions from different albums) you can hold the Alt or Option key (for Mac OS X) or the Shift key (for Windows) and chooseView > Show Exact Duplicate Items. This will show only duplicate songs having the same name, artist, and album.
You can find the full article here:
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