When you launch Akeeba Backup, it will try to determine the
permissions of the media/com_akeeba directory and
all its contents. If they are not 0755 for directories and 0644 for
files, it will try to fix those permissions automatically as they are
vital for the correct operation of the component. If you have enabled
Joomla!'s FTP mode in your site's Global Configuration page, Akeeba
Backup will automatically use it to fix those permissions. Some
servers, though, do not support using the SITE CHMOD command to
perform this change and will cause Joomla!'s FTP library to spit out
this error.
As long as you do not get a permanent big yellow warning box notifying you that the permissions need to be fixed and/or that jQuery is not properly loaded there is nothing to worry about. Unfortunately, there is nothing we can do to make this message disappear, as Joomla! itself does not give us an option to suppress such expected error messages.