[BUG] Claude Code accessing file location other than those it was given permission to use

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

While creating a python project where Claude had connected to my local GitHub repo instead of using the folder selected by me Claude on its own created its own branch and began to modify files in that location instead of the one it had been given access to.

While this new location was on the same physical drive it was at a different directory path than the path used for my GitHub repo's

What Should Happen?

Claude should only be able to read/write/modify files in the directory(s) I provide access to not in any other location.

Error Messages/Logs

Steps to Reproduce

As Claude did this on its own, without direction I am not sure how to reproduce it?

Maybe:

Step 1: Assign a repo folder to Claude Code
Step 2: Monitor and watch when it starts coding in another location than that folder?

Claude Model

Other

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

claude-sonnet-4-5-20250929

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

_No response_