Do you mean to say you were running Calibre and Sony software simultaneously? That's not a good idea. I generally avoid this problem by not running Sony's program at all.
I can't explain where the extra collections came from, it's never happened to me. However, it shouldn't be too hard to straighten out with Calibre. You could edit the metadata for each book, but I think it's be easier to directly edit the contents of the "Tags" and "Series" fields in the library mode. Just double click on the field and delete the extra values, or replace them/it with one of your choosing. Leaving one of these fields blank removes the book from the collection named for the value in the field.
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