If you have trouble searching your Papers 3 library either in the main library view or using Magic Citations try verifying your spotlight search index.
To do so, go to Help > Troubleshooting > Verify Spotlight Search Index.
In case the search index verification did not help, Papers will need to rebuild the search index it maintains.
To do so, go to Help > Troubleshooting > Rebuild Spotlight Search Index.
Please note that his can take a couple of hours to complete (and we haven’t yet made a progress bar for it I’m afraid), but it will depend on the size of your library. You can watch the Console app for messages to show what it is currently indexing (and give an idea of when it is finished).