Licensing systems are designed (presumably) to deliver an optimum outcome - a competent pilot.
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They probably were competent for the purpose of licensing. They just weren't competent enough for the purpose of their operation. In non-private flying, it is the OPC and Line Check that should determine whether a pilot is competent to carry out the role that his or her employers are paying for. The issue here is that in a number of corporate operations, because they are carried out under the flag or private flying, there is no oversight from the regulator! What's more, as the regulator doesn't get to determine who it regulates, it seems to me that casting blame in that direction is wrong.