Regardless of third party applications, if the system drive information is showing file system inconsistencies, there are a few possibilities. Try each of the following in order until the problem is fixed.
1) Empty the Trash and reboot your machine in Safe Mode. Once you login, reboot normally.
2) Boot into macOS Recovery (command+R at the chime). Repair your normal startup volume using Disk Utility. While you can do this "in live mode" during normal operation, it's not as reliable as checking the volume from your recovery partition in recovery mode.
3) Reindex your drive.
- Choose Apple menu () > System Preferences > Spotlight > The Privacy tab.
- Click the Add (+) button and select your boot volume from the sidebar (sometimes under devices)
- Wait 10 seconds. Select the same item and click the Remove (–) button to remove it from the list.
- Quit System Preferences. Spotlight will reindex the contents of the folder or disk.
4) If (3) doesn't work, then forcibly reindex your drive from the terminal using the following command (admin privileges required):
sudo mdutil -E /