The biggest and most common flaw is that S&OP meetings are oriented in the past.
This is a surprise, because by definition, ‘planning’ (Sales and Operations PLANNING) is for future.
The only reason one needs to refer to the past is for some guidance on the future.
However, the way most S&OP processes are structured, even those certified by the best process certification consultants, result in a majority of the time being spent rationalising what happened and making sure it does not happen again.
This time would be best spent on planning for the future (obviously while taking into consideration what happened in the past). The re-active orientation of most S&OP processes is perhaps its most visible weakness.