I think it happens when there is a collection that hasn't been synced all at one time. I did have the same issue but it stopped for me when I stopped letting calibre use tags as collections and began only syncing a complete series of books at once.
The downside for me is if a new book in a series comes out I have to remove all the books in that series and then sync the entire series again with the new book included.
Honestly not sure if it's a Calibre issue or a Sony issue but as long as I keep to the above rule it seems to work fine for me.
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