You have a Microsoft SharePoint Online site collection and a site hierarchy that span multiple levels. For example, a site collection contains a subsite, and the subsite contains another subsite.
The site collection is using the Team Site template, and the SharePoint Server Publishing Infrastructure is set to Active on the site collection. Or, the site collection was created through the Publishing Portal template.
On the Navigation Settings menu in Site Settings (under Global Navigation), you select Structural Navigation, and then you select the Show subsites check box.
You make changes to the master page by using Microsoft SharePoint Designer to increase the MaximumDynamicDisplayLevels property of the TopNavigationMenuV4 control to a value of 2 or more.
When you view the submenu on the top navigation bar in this scenario, you see only one site level.
In Office 365
To view the sites that aren't present on the submenu of the top navigation bar, browse to the site collection or subsite on the first level of the hierarchy to view the site on the submenu. Or, if you're using the SharePoint 2013 interface, you can use the managed navigation feature to work around this issue. For more information about managed navigation, see Overview of managed navigation in SharePoint Server 2013.
In Office 365 pre-upgrade
To view the sites that aren't present on the submenu of the top navigation bar, browse to the site collection or subsite on the first level of the hierarchy to view the site in the submenu.
This issue occurs after you receive the latest SharePoint Online service update. Microsoft is working to resolve the issue.