(R2014a) It happens on modified file since a recent commit. If a file is newly added to git, adding/removing keeps local copy.
Also after removing the file, revert local copy in Modified Files just have the delete file list removed, but no file is recovered.
But Manage Branches > Revert to HEAD help to reset to most recent commit.
Git is superior tool. I am so happy to see Git support in Simulink. Hope you guys make the best out of it.