It's the scripts with lots of bash features which don't really work properly in zsh. It has a bash emulation mode but it's not very good because bash is too complicated and quirky. They're missing too much stuff and some just doesn't behave in a proper bug-for-bug compatible way.
I don't really understand the point of the bash emulation mode. It's fairly dangerous to use it since many shell scripts can go horribly wrong from some minor issue due to the terrible error handling, etc.
I don't think it has issues with POSIX compliant bourne shell though.