There's just one scenario: a completely absent #! line.
It's an easy fix, just add the line, otherwise 0755 scripts with no #! do execute using the current shell.
That doesn't work for me (in Fish).
> 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.
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.