We have the git bare repository in unix that has files with same name that differs only in cases.
Example:
GRANT.sql
grant.sql
When
The simplest way to actually fix the issue is to rename one of the files so that they won't conflict on a case-insensitive file system like Windows or OS X.
Following a commit from the Linux/Unix system where you can most easily address the problem everything will be fine on Windows after a pull. To prevent this problem from occurring you would need to add a commit hook similar to what djjeck suggested.
The symptoms on Windows for this are very confusing and include:
Since both files can not coexist on a case insensitive platform you have to change one of the file names to avoid the trouble.