Is the user AD master user? If so have you checked the import tab as the user might be there? Also the user might have a missing attribute, as such the user is skipped when an import is triggered. You can check the System log (admin Dashboard->Reports->System Log) and in the search bar type Skipped. If you find a result with the user it will tell you there why the user has been skipped and what attribute is missing. If you require further assistance with this I recommend to open a case with Support and we can assist you with the troubleshooting.
Paul Stiniguta Technical Support Engineer Okta Global Customer Care