Overview
You want to create a user group in the MGR GUI, allowed to provision applications only. All users added to this group shall be allowed to "Activate, Deactivate, Delete" applications, so you set the privileges in the section SMS Applications for Applications only. 
After saving these privileges, the settings are gone. If you try setting all the rights for the SMS Applications and reduce these rights row-by-row using the checkboxes with saving actions in between, the rights for Applications are gone at a certain point, without logging any errors.
Information
This is a known issue that can be reproduced in MGR GUI versions previous to Release 19.4. In this case, you must update your MGR version to 19.4 or above.