>>8523656>>8523662Drilling of these pin holes are done manually at a drill press with the help of an alignment fixture to quickly align the parts. If the alignment fixture is inaccurate, the whole batch will have the same issue, until a new alignment jig is made.
Another popular case of this off my head is with FE Cliffjumper. The pin on one side of the chest was off-center, resulting in the early batches being unable to open up their chest fully.