Are the ones with black eyes, males?
if yes, it might be the same as male guppies whose eyes turn black when they are pissed off with another male. Guppy language, black eyes means your in for a fight
Black Mollies were bred to have black eyes. Some did, some didn’t, so, being human, they decided the black eyes were a desirable trait, and called those with black eyes “better quality”.
If they were born like this, it will remain this way. It means that instead of iridophores (silvery or blue color cells), the iris contains melanophores (dark color cells). Nothing to be worried about. This also happens with other kinds of ovoviviparous livebearers.