Too many files found

I have all my media on an external hard drive connected to my iMac (maybe 60 movies in quicktime format or ripped via MacTheRipper). When I import data, even though only my external drive is connected, Sapphire finds thousands of files–most of which I didn’t know existed and certainly not on my external hard drive. Some of the files may come come from my iMovie Projects and iMovie Events which I moved onto the external drive.
Any ideas?