repo.status() appears to be broken?

I'm running repo.status().items() in a pre-commit hook using the -a flag (git commit -a -m "Test"), and I get a result that looks like this:

[('config/git_hooks/pre-commit', 256), ('bin/run_flake8', 256)]

If I run git status in that same process, I get:

On branch ops_1331_fix
Your branch is ahead of 'origin/ops_1331_fix' by 2 commits.
  (use "git push" to publish your local commits)
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    modified:   bin/run_flake8
    modified:   config/git_hooks/pre-commit

In other words, pygit2 is reporting those files as not being staged, and git is reporting them as being staged. Why the discrepancy?

Start by reproducing the discrepancy with repo.status().items() in the pre-commit hook while using git commit -a, then compare its result with git status for the two listed files. Read the pygit2 status API and the related libgit2 behavior; done means explaining why staged files receive status 256 and correcting the mismatch if it is a bug.