Can you elaborate on the permissions? Did you overwrite the files?
Depending on how PHP is running (as apache module or php-fpm it runs under 1 user for all sites, when running as fastcgi it can run as the user for that domain - do note static content it still fetched by the webserver which runs as 1 user for all domains).
Thus if you run PHP as module and the permissions are say:
-rw------- then your user (the FTP user) can read the file - but the webserver can not. If it's running as fastcgi thus php should work, *however* and this is pretty important, as all static content (like jpg files etc.) is still served by the webserver these permissions won't work either as it can't read the static files.
Anyways many FTP clients allow you to set the default permissions to set after uploading files. Maybe it's just set to strict and maybe you just overwrite all the files. This would cause the client to change the permissions. But your post isn't very extensive on where it goes wrong exactly.