Ok, if these are "imperfections" (these bumps aren't plastic from the carts btw) then what could they be made out of?
It sure it is plastic after all. Maybe the molding process wasn't always perfect and instead of a plain surface it you got one that comprised some unevenness/coarseness, wich now makes itself visible through such bumps within a sticker's surface?
The other possibility is, that they are thin plastic particles, namely ones that broke from the edges of a fresh manufactured/assembled cart-shell and, through friction, became attached to the plain surface underneath the sticker or got pulled under the sticker, when it was electrically charged. The latter happens immediately after releasing a sticker from the paper that is holding it.
Check out some edges of Japanese Mega Drive boxes, (especially those from Taito) they often carry some thin plastic straws, that break up by themselves, leaving no visible traces. Something like that could got under an AES sticker, too.