Internal server error when accessing cloned rep

Using a private repo, I am having issues with a remote clone. After cloning, I receive a 500 internal server error on specific files (the same ones every time) when accessing them via webserver (repo is a web project). This also occurred when I did a git pull on the remote clone.

I used to simply copy the contents, delete the file, recreate via ftp gui, and paste the contents back in, and the error would disappear, but now it seems to be here permanently.