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Calibre only ever sends one file per book.
Your description sounds like you are using the Collections view on the Sony. With default Calibre settings a Collection is created from any tags in the books you send so in the Collections view it is not abnormal to see a book appearing in multiple categories.
In Calibre you can configure the Sony Device driver to control whether tags should create collections at the Sony level. To do this (with the Sony connected) Right-click on the Connect/Share icon to configure the driver.
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