IssueYou're using Managed Navigation in SharePoint 2013 and you've created navigation items that have subitems. In Term Store it would look like this (where Alisivu is the term that is not shown on the site):
For some reason, the navigation in your site doesn't show the sub-item.
ExplanationWhen you're on the site, subitems are visible. But as soon as you go to Site Settings, or other pages under _layouts, you will not see subitems. This appears to be a functionality carefully implemented in SharePoint, for you pleasure/confusion.
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