When performing a Discover scan, the scan will fail if it encounters too many consecutive Access Denied errors. The Discover server can be configured to ignore these errors so that the scan will complete successfully.
On the Discover server(s) in question, edit the crawler.properties file in the config directory. Change this entry to true:
filesystemcrawler.ignore.access.denied = true
Save changes to the file and recycle the Discover server from Enforce. Perform the scan again to see if the workaround has succeeded.