This probably isn't your problem but my buddy used to squeeze with the tip of his thumb causing the thumb to bend a little bit and put pressure on the knuckle.  His thumb holes was tight enough that it wouldn't allow the thumb to noticeably bend but it would cause the knuckle to rub and he wasn't coming out clean.  He finally realized he was subconsciously doing that and worked on keeping his thumb straight and not squeezing.  Are you getting and irritation, blisters etc. on or around your knuckle?

Not coming out of the ball clean can be caused by several things or a combination of them. Yes, improper span and pitches can contribute. Knuckling the ball can also be a cause. If you "grab" the ball because of a thumb hole that is too large you will need to bend your thumb in the hole and grip the ball too tightly causing you to have difficulty getting out of the ball. Early rotation of the hand can also cause you to grab the ball at the bottom resulting in the same thing. Assuming you have the proper fit on the ball, i.e. the span, pitches, and thumb hole are correct, then I would recommend using the "one step drill" to isolate on your release. Your thumb should be straight inside the ball and gently pinching the hole. During the drill, relax your thumb first at the ankle of your sliding foot and then rotate your hand slightly allowing the weight of the ball to transfer from the back of your hand toward your finger tips. Your fingers should exit the ball just in front of your toes. Once you have mastered this and know what it feels like to roll the ball off of your hand, add your approach back in at half speed while concentrating on rolling the ball.

Fran