I've noticed it's somewhat common with Saturn discs and even some Dreamcast games, they just naturally start developing pinprick-sized holes in them.
I've seen pinholes on Saturn and SegaCD discs frequently, but copies of the same games I've had since release don't exhibit any holes. I'm pretty sure that 99.999999% of all holes that appear on those games are due to mistreatment in some way, like people putting the label surface down on something a bit rough.
The screening on the top of SegaCD and Saturn games is suuuuper thin, making it easy to scratch the top data later part and have holes appear. I think if the pinhole issue was a widespread manufacturing issue there would be a lot more dead games out there.