It just happens because the core is not always exactly perpendicular "under" the pin. It can be shifted to the side, and since the CG is measured and marked after the ball is produced, its placement can easily fall out of the pin-MB line. For drilling, it is a good indication for the internal weight distribution, though. With a shifted CG you can e. g. avoid a balance hole, due to a beneficial internal structure of the ball.

Even the MB must not always me marked or measured correctly... pins used to mark it can be bent, and the De-terminator to measure it can also malfunction (just like CG measurement).

You never know...
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DizzyFugu - Reporting from Germany

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No, it won't affect ball motion.

The CG is only going to come into play when trying to get the ball to fall within USBC's static weight requirements.

As others have said, having a CG shift may or may not be suitable for RH or LH bowlers.  

To over simplify it, look for a CG shift that is opposite your handedness - left CG shift for right handers and vice versa.  This is usually because the MB is placed in a "strong" position (right of thumb for RH, and left for LH), and a CG more than an inch or "so" from grip center may need a weight hole to make the ball USBC legal.

Of course, extreme CG shifts can be very difficult to drill depending on the top weight of the ball and the desired layout and reaction, and extreme shifts will usually be labeled 2nds or blems.



** Note:  I may or may not know what I'm talking about.  I'm not a ball driller, but I play one in my garage!