There are two common pitfalls when working with FTP clients. Some programs hide system files by default, so e.g. .htaccess files are neither shown nor transferred. Since these files typically contain important Apache configuration settings, skipping them can be a serious security risk!
The second pitfall is a wrong transfer mode. If a binary file is transferred in ASCII mode, it is likely not to work correctly on the production server. Most of the professional FTP clients like WinSCP take care of the transfer mode automatically, which is another reason why you should always use one.