I had this same exact problem after taking a 2 month break to let an elbow injury heal. I couldn't figure it out because nothing felt different. My ball rolled the same; everything felt the same.
I decided it was time to buy a couple new balls and get refit to see if that would address the problem.
We did change my pitch from slightly reverse to 0, and I also made an attempt to stop using Magic Carpets at that time.
The bruising persisted. I also had formed a very small burn mark on the pad of my thumb directly under the nail portion. It was like a blood clot that was deeper under the skin than say a blister. That actually went away after a while even though the nail continued suffering.
The only thing that stopped the bruising of the nail was to completely stop gripping the ball through the swing. It still shows slight discoloration, which may just be related to me never quite letting it heal 100% since I bowl 5-10 games a week or more, but it is for certain neutralized. In a way I found this problem to be a blessing in disguise, since it helped force me to stop gripping at the bottom of the swing.
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There is nothing so easy to learn as experience and nothing so hard to apply