When the ApplicationMaster shuts down it's supposed to remove the staging directory, assuming properties weren't set to override this behavior. During shutdown the AM tells the ResourceManager that it has finished before it cleans up the staging directory. However upon hearing the AM has finished, the RM turns right around and kills the AM container. If the AM is too slow, the AM will be killed before the staging directory is removed.
We're seeing the AM lose this race fairly consistently on our clusters, and the lack of staging directory cleanup quickly leads to filesystem quota issues for some users.