Git can track the file permissions on your source. This can be good, but for small projects on a webserver where permissions change from time to time, and permissions on development app don't match or matter anyway, it's often easier to just skip this check alltogether. For the application in question look in the .git directory in the application root. You'll see a config file with the application specific directives. Open the file with your editor of choice and change the filemode to false. It's set to true by default.
[core] repositoryformatversion = 0 filemode = false