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.

To test: 

1. Add block Main menu
2. Configure the block to be displayed throughout the entire site
3. Enter into a course
4. Add an activity or resource into the course
5. The activity will not be in the course, It will be in the Main menu

Tested in Moodle 3.11.1 and in Sandbox