Kartik,
I couldn't say. In all the years I have been using SCM, I have never been able to prevent all such errors from occurring, I have only been able to solve certain problems only under certain specific instances. Usually, the 'solvable; problems I have seen are a result of poorly written enhancments or custom programs.
One might speculate that the reason SAP provides these repair programs (yes, there are MANY inconsistency-repair type programs) because they believe that such errors are inevitable.
Maybe you would be better served by just running such programs periocically in batch, as recommended by SAP.
http://service.sap.com/~sapidb/011000358700000955412003E
Best Regards,
DB49