When the block "Main menu" is added into a Moodle and configured to be displayed throughout the entire site, it's not possible to add activities or resources into a course, this activities or resources are added to the Main menu.
- Add block Main menu
- Configure the block to be displayed throughout the entire site
- Enter into a course
- Add an activity or resource into the course
- The activity will not be in the course, It will be in the Main menu
Tested in Moodle 3.11.1 and in Sandbox