SharePoint 2010 and SharePoint 2013 both have the same problem when you try to create a new Web Application. There is a timeout limit that occurs during the creation of the Web Application and the web application is provisioned only on the local server. The wwwroot folder for this web application is empty and all you can do is delete the application. You cannot create a site collection using this web application.
Microsoft says that his error occurs because more and more web applications are created on the same server (i have seen this error even when creating the fourth or fifth web application) and during the creation process IIS is reset and by default the application pool allows 90 seconds for the connections to close off before forcibly shutting down. When you have more than one web application apparently 90 seconds is not enough for the provisioning to finish. As a result the w3wp process is killed and the provisioning process is stopped prior to the timer jobs being created.
The solution is to open IIS manager on the server hosting the Central Administration:
1. in the tree view, expand the server name and click on Application Pools.
2. Locate the SharePoint Central Administration v4 application pool. Right click on it and choose Advanced Settings.
3. In the Process model section, set the Shutdown Time Limit to a greater value.
4. You can also set the idle shutdown to False.
5. Restart IIS