WOrng files within libraries

Hi,
Just installed PLEX server and followed the process to create a library; when I choose the folder that contains the files that I want, I can see all of them there, but when I hit the button to add the files, the program mixes everything and save some files from that folder, some of others, some are missing .... I have tried several times but always happens the same; how can I fix this?. I create 3 libraries and all behave the same
thanks in advance