In our case is was a capitalisation issue as mentioned above. We're working on OSX, which is ambiguous about the capitalisation of filenames. The process of upgrading the plugin changed the capitalisation of the Application folder, and Git split the folder into two. Presumably anything with changes went into the new folder with the lower case "a".
One way out is to delete the plugin folder, commit the change, then add the plugin folder back and commit again. Or you could use a filesystem that is truly case sensitive, like Linux, to do your commit.