Yeah. I've worked on enough cross-platform applications that it's always a big concern for me. Usually I tackle it by enforcing strict naming conventions across any application stack (which of course has other benefits).Case-sensitivity. It sucks, but most developers are uneducated regarding filesystems and filesystem-access, their experiences usually limited to Windows. They don't realize that case-sensitive makes a difference. Even character-encoding for filenames makes a difference. It's like the CJK-days all over again.
As application development as become (paradoxically) both more complex and easier to do, I've found that it's quite common for people to be working in a context entirely devoid from some of the fundamental aspects of computing; the file system, the shell, and communication (mostly encoding — the good ol' CJK days). So these problems crop up a lot, especially in internally built enterprise software and home-made applications.
Luckily enough, I find helping/teaching/mentoring fun, so I usually enjoy helping to address such issues