That's a different problem, though. /bin/sh must point to a sh-compatible shell. fish is not a sh-compatible shell. Therefore, any script using /bin/sh will never attempt to run as fish (as /bin/sh will never point to fish).
The reason I'm having a hard time imagining how a scripting system that relies on bash would fail with fish is because I can't imagine how one would actually write a script that is executed with the user's login shell. There's no #! line that would do that by accident.