Please explain what you mean by a duplicate file. In theory, there should be no exact duplicates of your files in any catalog. If you are talking about similar files e.g. those shot in bursts, or perhaps edited copies of files, then there are a number of possibilities to find and consolidate the files into stacks.
So how did you wind up with these duplicates? And why do you have more than one catalog?
@Walter_H's reply makes the most sense for what you are experiencing. So, we need you to confirm that as a possibility. Provide us with a screenshot (like Walter's) of your Watch Folders dialog which can be accessed via the File>Watch Folders menu. You should definitely not be placing your backup folders in a Watched Folder (and I also suggest that you not add files from Watch Folders automatically, because it looks like that is what has gotten you into trouble here.)
To try to provide some solutions, please tell us more about how you store your files. Are they all in the Pictures folder on your C drive or somewhere else?
How do you name the folders where the images are stored, e.g. by date or content?
Where are you storing your backups?
Another way we may be able to confirm whether your backups are the source of the duplicates is for you to do the following:
Press Ctrl+Shift+K. A search text box will appear.
Enter B00 into the text box and click OK.
How many files are now found in the grid? Make sure you are in Details View (Ctrl+D) and that File Names is checked on the View menu. Do all of the file names start with B00?
Make sure that your Folders panel is set to View as Tree. Does your backup folder location appear in the Panel?
And when you say you have more than one catalog, are these just backups of a single catalog or have you created more than one for other reasons?