OS X's filesystem is, by default, case-insensitive. So if you have two files in a Git repository with the same name but different cases you get the problem you're having now.
A simple work around is to use Disk Utility to create a case-sensitive disk image, clone the repo onto that, fix the problem there, and push the fix.
To make the disk image...
It will automatically be mounted and waiting for you in /Volumes. After you clone you should see both files and can do with them as you please.