Has This Happened To You ?

After a download is complete and I go to unzip it into a folder, I get this message "this file already exists, would you like to replace it?" I have tried answering no and yes to all and either way I have no success. I understand that you cannot have two files with same name, but if I look in the zip file that I downloaded I can plainly see there is several or more with same file name, setup included. Any help would be appreciated.