Then use zypper for your system admin. YaST SM also gives conflicts for updates unless one mitigates some of those with a setting. Apper is GUI for end users. Zypper is suitable for system administrators and not a GUI.
This has been discussed many times, here and on the mailing list, involving others making that very same point i.e addressing different types of user. Yet some posters (protesters mainly) conveniently ignore this, and do not qualify their opinions. IIRC there have been patches (maybe only one) recently to bring them in line on conflicts.
So what updates were you updating when the conflicts occured(?) I used Apper for all the standard updates for my system, plus Packman, and a couple of other additional repos (low number of infrequent updates). Not one conflict, I would have expected a few, but none. Maybe your setup is just more complex, and zypper gives you more control.