You don’t just copy files into the iTunes library directories on your computer.
See, the way it works is that you use your mouse to drag your media files into the Library area of an open iTunes application window. iTunes will then copy the files from their original locations over into the iTunes Library directories (unless you have it config’d to leave them in place). Once that copy operation is complete, iTunes then updates its database with information about those files, like where they are, what kind of star rating you gave them, when they were added, last played, etc.
The iTunes application window is showing you what it has in its database which, as you’ve discovered, is not just a plain old directory listing.
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You should treat the iTunes library directories as a read-only source… meaning that if you want to grab a copy of some song or movie, you can find it in there and copy it out if you want. But you should avoid making any modifications to the files or structure of the iTunes library directories as that will put them out of sync with where iTunes expects to find them (as mapped in its own database.)