christian w writes:

Sorry for the insufficient reproduction steps.

I managed to figure out it has something to do with git repos within
git repos. It happened to us because of go packages that are inside
our repo. These are the reproduction steps that work for me
consistently using Go version go1.14.4 darwin/amd64. This is the repo
that gets cloned into src/golang.org/x/debug by the go get command:
https://github.com/golang/debug/tree/66ec140f2f72d15dc6133502edd2bb7238b1740c

$ mkdir testdir
$ cd testdir
$ git init .
$ GOPATH=$(pwd) go get -u golang.org/x/debug/ || true
$ git ls-files --others '*.txt'#
src/golang.org/x/debug/

Okay, removing Go from the equation:

     $ # in fresh repo
     $ mkdir a
     $ git init a/d0
     $ touch a/f0.txt
     $ git ls-files --others 'a/*.txt'
     a/d0/
     a/f0.txt

It looks like the spurious a/d0/ entry doesn't show up until v2.27.0, in
particular 95c11ecc73 (Fix error-prone fill_directory() API; make it
only return matches, 2020-04-01).  Adding the author to the Cc.  (Sorry,
Elijah, I recall your frustration with dir.c from a previous ls-files
issue that I reported [1]).

[1] https://lore.kernel.org/git/CABPp-BFG3FkTkC=L1v97LUksndkOmCN8ZhNJh5eoNdquE7v9DA@mail.gmail.com/ (local)