This is plausible if you have scripts that do dumb shit like
eval "$SHELL ..."
because (at least sometimes?) $SHELL is set by your login program and not your shell, and dropping to an alternative shell by just typing
zsh
and hitting enter or whatever won't reset $SHELL.
You mention elsewhere that this had to do with a special OpenSSH setup, which also fits.
One of the things you can do with ssh-agent is use it to launch a child process with a dedicated SSH agent that (only) has certain keys on it, and which exits once its child exits. This is sometimes handy for deployment scripts or doing git checkouts or whatever because you can ensure you don't get locked out for too many auth attempts because the user just has too many extraneous keys on the agent associated with their normal user session.
If you were leveraging this feature for interactive shells, you might be tempted to use $SHELL to decide what executable to have ssh-agent launch, so that you could (for example) accommodate both bash and zsh users and let them launch a shell with a special SSH agent but which honors their usual preferences by loading their usual shell and reading their usual zshenv or bashrc or whatever it is.
You mention as well that you had to actually uninstall fish to get things to work again, and also that you were on macOS. I can't be certain about the cause here, but one obvious thing occurs to me:
macOS doesn't handle environment setup like any 'normal' (Linux or *BSD) Unix. On normal Unices, your login shell actually also launches your graphical user session, so to configure a session-wide environment variable, you just set it in your shell startup somewhere. On macOS, login shells are actually only used in SSH sessions and terminal emulators. If you want to set environment variables for apps that are not launched from terminal emulators, you have to use hacks (like Doom Emacs' env file, for example) or configure them for the whole user session via a LaunchAgent.
In the case of $SHELL, that environment variable is used by editors to determine what shell to use when you run external commands. Without it, if you are a fish user and you launch MacVim or Emacs (or, presumably, VSCode or anything else) from your dock, when you go to launch external commands, they will run not in fish but some other shell (probably zsh or bash). If your install method for fish tried to handle this for you (pkgsrc and Nix don't, but the .pkg from the developers or Homebrew might, idk), or if you dropped to bash only from terminal emulator windows that were already running fish instead of opening a new session for bash, you may have wound up in a bash session where $SHELL was still set to fish. That's the only reason I can think of for why you might have had to actually uninstall fish to get this ill-behaved script to work right.
Anyway:
1. As a user, pay attention to what $SHELL is.
2. As a script author, never use `eval "$SHELL ..." or equivalent`.
> macOS doesn't handle environment setup like any 'normal' (Linux or *BSD) Unix. On normal Unices, your login shell actually also launches your graphical user session, so to configure a session-wide environment variable, you just set it in your shell startup somewhere.
That's no longer true for Linux, at least. GDM launches stuff via systemd user sessions, which do not source your profile.
I'm not sure how I feel about it. The old way feels 'simple' to me, but the new way does mean that shell misconfiguration won't hose your GUI sessions.
You mention elsewhere that this had to do with a special OpenSSH setup, which also fits.
One of the things you can do with ssh-agent is use it to launch a child process with a dedicated SSH agent that (only) has certain keys on it, and which exits once its child exits. This is sometimes handy for deployment scripts or doing git checkouts or whatever because you can ensure you don't get locked out for too many auth attempts because the user just has too many extraneous keys on the agent associated with their normal user session.
If you were leveraging this feature for interactive shells, you might be tempted to use $SHELL to decide what executable to have ssh-agent launch, so that you could (for example) accommodate both bash and zsh users and let them launch a shell with a special SSH agent but which honors their usual preferences by loading their usual shell and reading their usual zshenv or bashrc or whatever it is.
You mention as well that you had to actually uninstall fish to get things to work again, and also that you were on macOS. I can't be certain about the cause here, but one obvious thing occurs to me:
macOS doesn't handle environment setup like any 'normal' (Linux or *BSD) Unix. On normal Unices, your login shell actually also launches your graphical user session, so to configure a session-wide environment variable, you just set it in your shell startup somewhere. On macOS, login shells are actually only used in SSH sessions and terminal emulators. If you want to set environment variables for apps that are not launched from terminal emulators, you have to use hacks (like Doom Emacs' env file, for example) or configure them for the whole user session via a LaunchAgent.
In the case of $SHELL, that environment variable is used by editors to determine what shell to use when you run external commands. Without it, if you are a fish user and you launch MacVim or Emacs (or, presumably, VSCode or anything else) from your dock, when you go to launch external commands, they will run not in fish but some other shell (probably zsh or bash). If your install method for fish tried to handle this for you (pkgsrc and Nix don't, but the .pkg from the developers or Homebrew might, idk), or if you dropped to bash only from terminal emulator windows that were already running fish instead of opening a new session for bash, you may have wound up in a bash session where $SHELL was still set to fish. That's the only reason I can think of for why you might have had to actually uninstall fish to get this ill-behaved script to work right.
Anyway:
1. As a user, pay attention to what $SHELL is.
2. As a script author, never use `eval "$SHELL ..." or equivalent`.