I had this error in a test Content Management environment of Sitecore 8.2 Update 2. And it was spamming our logs every 5 minutes.

5564 09:01:10 FATAL [Path Analyzer](ApplicationContainer.GetInstance) Can't create instance using path 'pathAnalyzer/webRequestFactory'. Make sure the referred element is present in configuration
5564 09:01:10 ERROR Exception when executing agent pathAnalyzer/newMapAgent
Exception: System.NullReferenceException
Message: Object reference not set to an instance of an object.
Source: Sitecore.PathAnalyzer
   at Sitecore.PathAnalyzer.Data.Remote.RemoteTreeDefinitionService.BuildRequest(String requestPath, HttpMethod requestMethod, Byte[] requestData)
   at Sitecore.PathAnalyzer.Data.Remote.RemoteTreeDefinitionService.GetAllDefinitions()
   at Sitecore.PathAnalyzer.Processing.Agents.NewMapAgent.GetTreeDefinitions()
   at Sitecore.PathAnalyzer.Processing.Agents.BuildMapAgent.Execute()
   at Sitecore.Analytics.Core.BackgroundService.Run()

The reason for us was a stray configuration file which we didn't need!
Sitecore.PathAnalyzer.RemoteClient.config was enabled while we didn't have a Remote Client.
Additionally, when opening the Path Analyzer in Sitecore, we didn't see anything loaded.

Just removing this file solved our problem.