If you are asking for help, provide lots of detail so problems can be reproduced.
Things to describe:
Operating system ATutor is installed on -Ubuntu 14.04.1
ATutor version - 2.2
Patch #s applied - 0001, 0002, 0003, 0004, 0005, 0006, 0007, 0008, 0009, 0010, 0011, 0012, 0013, gg0005
ATutor theme name - Atutor (default directory)
PHP version - 5.5.9-1ubuntu4.5
MySQL version - 5.5.41-0ubuntu0.14.04.1
Webserver & version - Apache/2.4.7
Copies of error messages - there is no error message
Changes to default settings - 'Require Email Confirmation Upon Registration' set to enabled
Web browser being used - Firefox 38.0.1
...and anything else relevant -
I check Manage-> File Manager as you suggested, deleting files is fine there. In file storage after I click on 'Delete' button, it supposed to display the message says 'Are you sure to delete ...', but it even does not shows this message. So I think it seems not to be file permession.