The problem is visible in Windows/Mac toolchains - they run on filesystems that are NOT case sensitive. Problematic files are part of Linux Kernel: include/uapi/linux/netfilter/ e.g. xt_mark.h vs xt_MARK.h During extraction they can either get overwritten, skipped (ignored) or renamed, depending on application and parameters. Should we put that into linux kernel bug tracker? I just checked and the problem still persists in v3.19.
This is really a CANTFIX. Certainly you could file a bug with the kernel upstream but they will most likely shrug and say "don't use windows". Its not something the Yocto Project can do much about either. This is just one of the downsides to using Windows toolchains and there isn't much we can do about it.
Can it be added a note in the documentation stating that the filesystems not case-sensitive will fail under this situation?