Shelby inspected every car Smith built. That's why you see the difference in the numbers. Not all cars were immediately "accepted". Often times, these were things AOSmith had no control over.
This led to some "discussions". The other side of this conversation is the business relationship. Someone had to pay for corrections, updates and changes. Often times, AOSmith was slow to be paid. This three headed relationship (Ford/Shelby/AOSmith) ultimately led to the end of the program. One of the main reasons there were no cars after 1969 was that AOSmith declined to build them. I can only surmise that was due to this dysfunctional relationship.