For some reason your server believes that there's a .htaccess file in that folder. I have seen it happen before where it's been there but hasn't been visible because the server is set to ignore "hidden" files (hidden files are defined by their file name startign with the full-stop like this). I've missed a few of them myself thanks to incorrect settings on file and FTP browsers. All that I can say is that your server does believe that the file exists if it really isn't there, so you'll need to figure out why that is. That's a server problem.
If you think that the file at wp-includes/vars.php is not correct them re-download a new un-touched copy of WordPress and re-install that file. If there is a problem with that I'd suggest doing it with every file.. if one's been changed somehow then there's no telling if any others have or have not been affected as well.