Microsoft has made errors concerning the WSUSSCN2.CAB catalog file, yes. Usually we work around through a static definition.
Windows Update not detecting installed updates correctly might have to do with the different branches of updates in existence. There are GDR (General Distribution Release) and LDR (Limited Distribution Release, the old name was QFE - Quick Fix Engineering). LDR updates without a GDR counterpart (or GDR satisfaction stub) might trigger WU/MU to install the GDR one although it's not required.