Git repositories can experience file name conflicts under specific conditions related to file name casing. Git tracks files based on their full path and name, but whether conflicts occur depends heavily on the underlying operating system's file system. Case-sensitive file systems (like most Linux setups) treat File.txt and file.txt as distinct files. Git fully supports tracking both independently. However, case-insensitive file systems (common on Windows and macOS) see these names as identical. When merging branches containing files differing only by case, Git may overwrite one file with the other without warning on such systems.

For example, if one branch adds Config.json and another branch adds config.json, developers on case-sensitive systems can commit both files. But when contributors using Windows pull or merge these branches, Git or the OS might treat them as the same file, leading to unexpected overwrites or loss of one version. This is problematic in web projects sharing assets (logo.PNG vs Logo.png) or software projects with code files using different casing conventions across branches. Tools like Git for Windows attempt to warn users, but limitations remain.

The primary limitation is silent data loss or corruption on case-insensitive systems during merges or checkouts, posing significant risks to collaborative workflows. Developers must proactively enforce consistent naming conventions across the team. Future solutions may involve stricter Git hooks or improved cross-platform handling, but awareness remains crucial to avoid this hidden hazard impacting project integrity.