What did you do before the bug happened? (Steps to reproduce your issue) mkdir repo cd repo git init "sample file" > file.txt git add file.txt git commit -m "Added file.txt" git checkout -b other_branch echo other file > other_file.txt git add other_file.txt git commit -m "Added other_file.txt" git checkout master echo Other file > Other_file.txt git add Other_file.txt git commit -m "Added Other_file.txt" git merge other_branch git status What did you expect to happen? (Expected behavior) A clean state, no unstaged changes. What happened instead? (Actual behavior) There is always an unstaged file other_file.txt which case changes if I try to discard and the unstaged change stays. If I try to delete the file, I get two unstaged file removal changes. What's different between what you expected and what actually happened? The state should be clean. It looks like the merge process broke something due to the casing. Anything else you want to add: Please review the rest of the bug report below. You can delete any lines you don't wish to share. [System Info] git version: git version 2.28.0.windows.1 cpu: x86_64 built from commit: 77982caf269b7ee713a76da2bcf260c34d3bf7a7 sizeof-long: 4 sizeof-size_t: 8 shell-path: /bin/sh uname: Windows 10.0 18363 compiler info: gnuc: 10.2 libc info: no libc information available $SHELL (typically, interactive shell): <unset>