Manuscripts keeps around bibliography data after paragraphs citing it have been removed. This is done for several reasons, most important being that bibliography data may have become only temporarily unreferenced when paragraphs citing it were removed from the document (and something similar may be written again), and conversely you may have inserted bibliography data to your manuscript from a file or a reference library in order to cite it later, and simply have not done so yet.
However, if the bibliography data included in your manuscript is starting to get cluttered, you certainly can also clean it up with Manuscripts. Here's how:
- Go to Window > Show Bibliography Data.
- Right-click in the bibliography window that opened, and choose "Select All Unreferenced".
- Right click again and choose "Delete" (or you could choose to delete only the specific item you know to be unreferenced of course).
If the bibliography and citations did not automatically update, choose Format > Refresh Citations from the main menu.