In SharePoint 2013 when creating sub-sites (at least through the UI), and you set the new sub-site to inherit the global nav from the parent site, and the parent site uses managed navigation, you will find that the global nav of the sub-site does not correctly inherit all the managed navigation links from the parent site.

This has been reported by the links below:

http://blog.jussipalo.com/2013/03/sharepoint-2013-managed-navigation-not_12.html
http://social.msdn.microsoft.com/Forums/en-US/sharepointgeneral/thread/87a00e4f-59eb-4e36-a7f0-6535bb1f748a

You can fix this by re-applying the navigation settings of the new sub-site after it has been created (as discussed in the first link).

However, when you are provisioning many sites, you may want to fix this by code. Put the code below in a feature receiver and activate the feature for each sub-site:

var web = properties.Feature.Parent as SPWeb;
var rootWeb = web.Site.RootWeb;

var rootWebNavSettings = new WebNavigationSettings(rootWeb);
var thisWebNavSettings = new WebNavigationSettings(web);

thisWebNavSettings.GlobalNavigation.Source = StandardNavigationSource.InheritFromParentWeb;
thisWebNavSettings.GlobalNavigation.TermStoreId = rootWebNavSettings.GlobalNavigation.TermStoreId;
thisWebNavSettings.GlobalNavigation.TermSetId = rootWebNavSettings.GlobalNavigation.TermSetId;
thisWebNavSettings.Update();

The WebNavigationSettings class is defined in the Microsoft.SharePoint.Publishing.Navigation namespace of the Microsoft.SharePoint.Publishing.dll.