Not a Mac person, but if you moved the files from "master" folder to a subfolder than they should not longer be in master folder. If you copied them to the subfolders they should be in both places.
Have no idea why Finder sees them in both places if they were moved. Does not make any sense to me. Does Finder have a cache or need to be refreshed to see the current file setup?
Bridge should see the samething as Finder, they are both essentially the same type of application. The question is really what are we seeing in Bridge and what are we seeing in Finder. Maybe from a certain point of view they are both showing things correctly, depending on what really going on in with the files and with the settings of each application.
Could you post a screen shot of both Finder and Bridge showing this "master" location.