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.
It's an easy fix, just add the line, otherwise 0755 scripts with no #! do execute using the current shell.
> cat foo
echo wat
> ./foo
Failed to execute process './foo'. Reason:
exec: Exec format error
The file './foo' is marked as an executable but could not be run by the operating system.
Unless you want to define "bad" as "ignorant of some facet of computing" in which case we all fit.