why has itunes moved my music files out of the Music folder?

To my horror I just found out that itunes has moved folders (albums) out of the Music folder, Ive always found those folders very well organized (music, movies, podcasts, etc) now Im seeing some albums mixed with those folders (out of the music folder) and some albums IN the music folder as well, even worse I have the same folder inside Music and out!! with a few tracks on each, but in iTunes everything looks normal and it plays the album as usual, Im losing my mind over this I cant find a way to fix it, I even started moving them manually but there are too many, and for the duplicate folders I have to move the tracks that were moved. Any idea on why did this happen? I dont want to move the folders and lose hours only to find out that itunes did it again!! I thank you very very ver much in advance.