I never heard of this being a problem before...

[–] jobes 2 points (+2|-0)

Someone probably signed a big $$ deal to make a device which can analyze the baseballs far more in depth to prompt this question, but if that was the case, then shouldn't they hook that up to the assembly line and only keep balls that pass specific tests/thresholds?

The way manufacturing Works nowadays you figure they should be able to make it to whatever tolerances they need. It might just be that they can't find a way to do that in a cost-effective manner given how many baseballs they use in a game, balls going in to stands excetera.

[–] jobes 1 points (+1|-0)

Beyond that, it implies that as long as the balls are handmade and comprised of natural materials

Well, there is the problem. They aren't machine made