.htaccess file should be removed on uninstall

drush uninstall advagg -y

The following modules will be uninstalled: advagg
Do you really want to continue? (y/n): y
rmdir(/var/aegir/platforms/7/servers/sng-contrib/sng-oa-core-d7-1/sites/t2.socialnicheguru.com/files/advagg_css):[warning]
Directory not empty file.inc:2446
rmdir(/var/aegir/platforms/7/servers/sng-contrib/sng-oa-core-d7-1/sites/t2.socialnicheguru.com/files/advagg_js):[warning]
Directory not empty file.inc:2446

the .htaccess file is the only one enabled