System keeps booting into recovery after upgrading to El Capitan
Try booting it into Recovery and use Disk Utility to verify the disk it see if we have any problems there.

Hold these keys until the Apple logo appears. After your computer finishes starting up, you should see a desktop with an OS X menu bar and an OS X Utilities window with the options listed above. If you see a login window or your own desktop instead of the Utilities window, it's possible that you didn't press Command-R early enough. Restart your computer and try again.