as per my opinion you contain viruses inside your pendrive.some of the virus automatically changes the status of your some existing files into system files & thus they are not shown to users system file is hidden and protected.
try this:-
got control pannel>user accounts>
cilck option “view” into main upper pannel.
select " show hidden files" from option menu .then
unchek the box of "hide system operated files(recomended) option.
after doing both things click O.K.
now open your pendrive
you will see many files which were not previously visible to you.