Bj,
I think what happened was, whoever drilled the ball first, managed to drill into the core which has a void in it...purposely. That's the way the core is designed! Then on top of that, they managed to just angle the balance hole so that it touched that same void, and now you have a thruway!! The smaller hole near the thumb is normal. That's a suction release hole, so you can get out of the ball cleanly without your thumb sticking!
As for getting it plugged.....hmmmm, I don't know. But good luck with it.