A couple of thoughts:

 - There are some variations on the ZIP theme, but I wasn't aware of any
   generally compatibility problems these days.
 - Different operating systems (including commonplace ones like Mac OS
   9, Mac OS X, UNIX/Linux, Windows) have different "allowable" sets of
   filenames. E.g. Mac OS 9 and HFS cannot cope with ':' in a filename,
   while UNIX can't cope with '/'. (And there isn't enough room to
   enumerate how many characters are disallowed by DOS.) Perhaps, when
   moving files between different operating systems, the various ZIP
   programmes aren't quite smart enough to cope with this 'unforeseen'
   issue.