Thank you for the suggestion, Jon. Cleaning theme cash had the same results. In our case, we coudn't see the "Add activities and resource" link at all.
I was able to solve it by comparing the User roles with another Moodle website.
When I went to this specific course and I checked the Course administrations - Users - Permission I noticed that some user roles were Prohibited, including Authorized user role.
I changed Prohibited with Not set for all these occurences in Authorized user role and then it worked. (this is in Site administration - Users - Permissions - Define roles - click on Authorized user gear to edit it)
Somehow those permission got messed up on this specific Moodle site. A 5 minute solution after many hours of searching