Strange behaviour in git worktree setup

[svartkanin]

Troubleshoot

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Context
When using git worktrees the pre-commit hook has some strange behaviours. I have a pre-commit hook that may create a new file based on yarn build output but it can also be reproduced with the following snipplet in the .husky/pre-commit file in a git worktree setup.

cd subfolder
touch test.txt
echo "1234" > test.txt
git add test.txt

When running a commit git commit -am "test" the hook will suddenly create a file test.txt in the root directory and in the subfolder as well. Also the test.txt in the root is added to the commit but then deleted which results in the following status right after running the git commit command

git status
On branch husky-wt-poc

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	deleted:    ../test.txt

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	test.txt

no changes added to commit (use "git add" and/or "git commit -a")

Expected behaviour

The expectations with a git add test.txt in the pre-commit would be that the file created in subfolder/test.txt is added and that no test.txt is created in the root.