If you add more than one content query Web Part to the Rich Content zone in a Microsoft SharePoint Online environment, the content query Web Part is removed, as in the following scenario:
A user edits the home page of a publishing site and adds multiple content query Web Part to the Rich Content zone.
The user enters text after the first content query Web Part.
The user adds another content query Web Part.
In this scenario, the text and the second Web Part are included in the first Web Part’s div tag. The text and the second Web Part are removed if a third Web Part is added at the bottom of the Rich Content zone.
This issue has been fixed in SharePoint Online.