In the most obstinate cases with APFS disks, you may need to use the lower-level fsck_apfs command-line utility to verify and repair the APFS volume from the Recovery mode.
Similarly, for HFS+ disks, you may need to use fsck_hfs. Beside verifying, you can use it to repair the HFS+ catalog file. WARNING: this operation may not be safe for your data! You should make a full backup of your disk before trying. Please seek professional help on the matter.