1. It maybe caused by the similar photos, To protect the security of users data, Cisdem will not auto mark similar photos for deletion, which will only auto mark exact duplicates for deletion. If you just click Delete when the scan is finished, then it will only delete the exact duplicates.
To auto select the similar photos for deletion, you can run Cisdem Duplicate Finder and scan your photo library again, in the scan result interface, press Command+A to select all the photos in the left side list, click Smart Select on the right side, and then click Delete.
2. Is the synchronization process between iCould and your local device in progress? If yes, you had better wait until the synchronization process is completed and then drag your local photo library into Cisdem to scan again.