I haven't investigated too deep into this, but I've figured out a few
things.

First of all, to reproduce the issue:

- Install fish.

- Run `guix build --check fish`, it should output something like

  #+BEGIN_SRC sh
  > guix build --check fish
  Building /gnu/store/g9ra27952ay2a7j3mn7yp13b7m18kl1b-fish-2.7.1.drv - x86_64-linux
  grafting '/gnu/store/vgrav12zra9zky21ahm4x1qg8g4v58fj-fish-2.7.1' -> '/gnu/store/avk637800w1n7z1z0hnzx80r0fpd6729-fish-2.7.1'...
  /gnu/store/avk637800w1n7z1z0hnzx80r0fpd6729-fish-2.7.1
  #+END_SRC

- The graft source is a dead GC item:
	#+BEGIN_SRC sh
	> guix gc --list-dead | grep vgrav12zra9zky21ahm4x1qg8g4v58fj
	/gnu/store/vgrav12zra9zky21ahm4x1qg8g4v58fj-fish-2.7.1
	#+END_SRC

  Collect it:
	#+BEGIN_SRC sh
  guix gc --delete /gnu/store/vgrav12zra9zky21ahm4x1qg8g4v58fj-fish-2.7.1
	#+END_SRC

- Start fish:
  #+BEGIN_SRC sh
  > fish
  fish:
  echo $_ " "; __fish_pwd
                 ^
  in command substitution
          called on standard input
  ...
  #+END_SRC

I think Ricardo got a hunch of what's happening, except that it's not
about cache files in the user home's directory.  Instead, Fish seems to
record the path to the graft source.  A grep in the fish folder does not
seem to reveal anything, nor does `strings
/gnu/store/...-fish.../bin/fish`.

Could this be a grafting issue?  Like what was recently mentioned about
Racket?

Otherwise, as Meiyo pointed out, the solution might lie in patching
fish.cpp if grafting is not responsible for this.

--
Pierre Neidhardt
https://ambrevar.xyz/