That's usually caused by having your hand on the side of the ball early. Stay behind the ball until your ankle.
Seriously, if you had the ball drilled with no thumbhole, then added a thumbhole later, I doubt it's worth much with either style. You'll probably be best off at this point if you plug all three holes and get the ball re-drilled.
Why? If the thumbhole was put in to fit his hand, what is the point of plugging and redrilling the same way?
You're asking me to remember long-ago conversations with
Pro Shop guys, so I can't vouch for any degree of accuracy.
(I always wound up getting a thumbhole drilled at purchase--I'm used to it, and the feel of it on my palm helps ensure the ball is placed in the same spot every time--so I've never had to
deal with this particular problem. I've been informed sternly that I shouldn't get the ball drilled with no thumbhole with the idea of putting one in later, though.)
The point IIRC is that the thumbhole also acts as a giant weight hole, so drilling without a thumb gives a different CG and requires a different set of measurements.