OS X apps that 'shell out' to the BSD under-pinnings could be an issue. The CLI options can differ between Linux and BSD/Darwin.
If a program calls '/usr/bin/nc' and expect BSD options, it's not going to get them. "Replace GNU coreutils with BSD coreutils" is an option, but not one that everyone would be ready to jump at, because now things running on your Linux system that expect GNU options won't be getting them.