Any file considered to be "music" (and thus viewable in the music player) can end up being marked in an internal database as being a "ringtone" as well if you hit that "Use as ringtone" button. There is pretty much no built-in method to un-mark this.
I got tired of not being able to remove these accidental ringtones, so I put a (free) solution up on the market. "Ring Remover" does nothing but offer to remove the "is ringtone" status of any media that are both "music" and "ringtone". (It'll leave the file there, so you can still play it as music.)
(If you downloaded ringtones, or put things in an explicit ringtone directory, you need a different solution -- involving physically deleting the files -- since the file scanner will just recreate the ringtone status everytime you restart or re-insert the SD card.)