lyretails. I would guess that the trait of lyretail as opposed to regular tail is recessive. But that doesn't explain how a parent could be lR if l stood for the recessive lyretail and R for the dominant regular gene. Non-recessives may have a better survival potential, but not to that extent.
How long had you had both fish? Was this the female's first drop? Could it be that she was carrying the results of previous matings in a pet shop, wholesalers or even fish farm?
If that is the case, keep allowing the molly parents to mate and maybe save and raise their third batch. That would more closely resemble them and what you want.
If you have had both breeders for six months or so, that blows that theory to smithereens. ;) Then I have no clue what happened.
As for the popeye, either from the Guppylog Immediate Help section on popeye (Whoo-hoo! IH works in that case! See the second entry especially) or from elsewhere, I'm sure that you are aware that popeye is a result of water which isn't quite as clean as it should be. Popeye isn't a disease so much as a sign of other problems. Often because of a bacterial build-up, fluid builds up behind the eye. (Hummm... in some cases it can also be viral and the only thing we can do is militantly make sure the water is good and temperatures are consistent.) In fry grow-out tanks it is so easy to fall a little behind with partial water changes as those fish ravenously go through food and grow.
On the one hand (and I always figuratively look in the mirror as I say this) pick up the water changing a bit with the youngsters. You may indeed want to isolate and maybe euthanize that fish.
Oh! Look to see if there is a parasite in the eye. That too can be dealt with. (Arragh and this is written about breakfast time.) If need be, that fish could be treated for Diplostomum or eye fluke. (A fluke is a kind of worm and these species specialize in eyes.)
Sometimes the afflicted eye may even pop out and be lost. Get it out of the tank quickly if that happens. Ironically the empty eye socket may heal and the fish is less of a threat to infect others. One-eyed fish have to work a little harder to feed, but in the relatively benign environment of an aquarium it can still thrive.
And the problem was probably not genetic but environmental. If need be, that fish could even be used as a breeder, though I probably wouldn't if there were whole siblings of the same gender and strain available.
Please let us know what is happening with the adults. You may want to pass that first generation on as regular tailed mollies.
All the best!