-In Worksite Setup, select some site and click on Edit. Now select Manage Tools.
-From the right hand side menu that shows all the Selected tools, remove some tools that have different instances (like Lessons Pages and Web Content).
-Click on Yes when it asks for remove configured tool and it will disappear from the list. But it still remains checked in the left hand side under General menu and hence does not get removed when you click on Save.
-This replicates for the News tool also.(anything with sub-content).
Please find attached a screenshot of the same.