The specific issue was to do with a script we had to run to gain ssh access to an internal network. I can't post the script, but it was related to openssh.
Even logging into bash and running the script didn't work, I had to remove all fish binaries, symlinks, etc and set my shell to bash/zsh. Maybe it was an issue with how I installed fish, but yeah like I said, very strange, but I can vouch that I've encountered a similar issue before
It's a real shame because I think the fish syntax alone is worth the switch, for my personal machine(s) I use it.
Edit: this was years ago now, about 4 years, maybe the issue doesn't exist anymore but it caused me a bit of grief at the time (beacuse I didn't know it was related to using fish!), I've not since tried it again. I might try again and get back to this thread